HEADER HYDROLASE 11-MAR-26 11SY TITLE CRYO-EM STRUCTURE OF SUBSTRATE ENGAGED P97-UFD1-NPL4-FAF1 COMPLEX TITLE 2 (NPL4 FOCUSED) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR PROTEIN LOCALIZATION PROTEIN 4 HOMOLOG; COMPND 3 CHAIN: G; COMPND 4 SYNONYM: PROTEIN NPL4; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UBIQUITIN; COMPND 8 CHAIN: H, I, J, K; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: UBIQUITIN RECOGNITION FACTOR IN ER-ASSOCIATED DEGRADATION COMPND 12 PROTEIN 1; COMPND 13 CHAIN: P; COMPND 14 SYNONYM: UBIQUITIN FUSION DEGRADATION PROTEIN 1,UB FUSION PROTEIN 1; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NPLOC4, KIAA1499, NPL4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UBC; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: UFD1, UFD1L; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS ERAD, UBIQUITIN, AAA+ ATPASE, UNFOLDASE, HYDROLASE EXPDTA ELECTRON MICROSCOPY AUTHOR Z.LIAO,A.MARTIN REVDAT 1 22-APR-26 11SY 0 JRNL AUTH Z.LIAO,C.ARKINSON,A.MARTIN JRNL TITL FAF1 ACCELERATES P97-MEDIATED PROTEIN UNFOLDING BY PROMOTING JRNL TITL 2 UBIQUITIN ENGAGEMENT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.280 REMARK 3 NUMBER OF PARTICLES : 20565 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 11SY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-26. REMARK 100 THE DEPOSITION ID IS D_1000305972. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : CRYO-EM STRUCTURE OF SUBSTRATE REMARK 245 ENGAGED P97-UFD1-NPL4-FAF1 REMARK 245 COMPLEX (NPL4 FOCUSED) REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.60 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 17244 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H, I, J, K, P REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET G -2 REMARK 465 GLY G -1 REMARK 465 GLY G 0 REMARK 465 GLY G 1 REMARK 465 ALA G 2 REMARK 465 GLU G 3 REMARK 465 SER G 4 REMARK 465 ILE G 5 REMARK 465 ILE G 6 REMARK 465 ILE G 7 REMARK 465 ARG G 8 REMARK 465 VAL G 9 REMARK 465 GLN G 10 REMARK 465 SER G 11 REMARK 465 PRO G 12 REMARK 465 ASP G 13 REMARK 465 GLY G 14 REMARK 465 VAL G 15 REMARK 465 LYS G 16 REMARK 465 ARG G 17 REMARK 465 ILE G 18 REMARK 465 THR G 19 REMARK 465 ALA G 20 REMARK 465 THR G 21 REMARK 465 LYS G 22 REMARK 465 ARG G 23 REMARK 465 GLU G 24 REMARK 465 THR G 25 REMARK 465 ALA G 26 REMARK 465 ALA G 27 REMARK 465 THR G 28 REMARK 465 PHE G 29 REMARK 465 LEU G 30 REMARK 465 LYS G 31 REMARK 465 LYS G 32 REMARK 465 VAL G 33 REMARK 465 ALA G 34 REMARK 465 LYS G 35 REMARK 465 GLU G 36 REMARK 465 PHE G 37 REMARK 465 GLY G 38 REMARK 465 PHE G 39 REMARK 465 GLN G 40 REMARK 465 ASN G 41 REMARK 465 ASN G 42 REMARK 465 GLY G 43 REMARK 465 PHE G 44 REMARK 465 SER G 45 REMARK 465 VAL G 46 REMARK 465 TYR G 47 REMARK 465 ILE G 48 REMARK 465 ASN G 49 REMARK 465 ARG G 50 REMARK 465 ASN G 51 REMARK 465 LYS G 52 REMARK 465 THR G 53 REMARK 465 GLY G 54 REMARK 465 GLU G 55 REMARK 465 ILE G 56 REMARK 465 THR G 57 REMARK 465 ALA G 58 REMARK 465 SER G 59 REMARK 465 SER G 60 REMARK 465 ASN G 61 REMARK 465 LYS G 62 REMARK 465 SER G 63 REMARK 465 LEU G 64 REMARK 465 ASN G 65 REMARK 465 LEU G 66 REMARK 465 LEU G 67 REMARK 465 LYS G 68 REMARK 465 ILE G 69 REMARK 465 LYS G 70 REMARK 465 HIS G 71 REMARK 465 GLY G 72 REMARK 465 ASP G 73 REMARK 465 LEU G 74 REMARK 465 LEU G 75 REMARK 465 PHE G 76 REMARK 465 LEU G 77 REMARK 465 PHE G 78 REMARK 465 PRO G 79 REMARK 465 SER G 80 REMARK 465 SER G 81 REMARK 465 LEU G 82 REMARK 465 ALA G 83 REMARK 465 GLY G 84 REMARK 465 PRO G 85 REMARK 465 SER G 86 REMARK 465 SER G 87 REMARK 465 GLU G 88 REMARK 465 MET G 89 REMARK 465 GLU G 90 REMARK 465 THR G 91 REMARK 465 SER G 92 REMARK 465 VAL G 93 REMARK 465 PRO G 94 REMARK 465 PRO G 95 REMARK 465 GLY G 96 REMARK 465 PHE G 97 REMARK 465 LYS G 98 REMARK 465 VAL G 99 REMARK 465 PHE G 100 REMARK 465 GLY G 101 REMARK 465 ALA G 102 REMARK 465 PRO G 103 REMARK 465 ASN G 104 REMARK 465 GLN G 562 REMARK 465 LEU G 563 REMARK 465 PRO G 564 REMARK 465 GLY G 565 REMARK 465 LEU G 566 REMARK 465 HIS G 567 REMARK 465 GLU G 568 REMARK 465 TYR G 569 REMARK 465 GLY G 570 REMARK 465 ALA G 571 REMARK 465 VAL G 572 REMARK 465 GLY G 573 REMARK 465 GLY G 574 REMARK 465 SER G 575 REMARK 465 THR G 576 REMARK 465 HIS G 577 REMARK 465 THR G 578 REMARK 465 ALA G 579 REMARK 465 THR G 580 REMARK 465 ALA G 581 REMARK 465 ALA G 582 REMARK 465 MET G 583 REMARK 465 TRP G 584 REMARK 465 ALA G 585 REMARK 465 CYS G 586 REMARK 465 GLN G 587 REMARK 465 HIS G 588 REMARK 465 CYS G 589 REMARK 465 THR G 590 REMARK 465 PHE G 591 REMARK 465 MET G 592 REMARK 465 ASN G 593 REMARK 465 GLN G 594 REMARK 465 PRO G 595 REMARK 465 GLY G 596 REMARK 465 THR G 597 REMARK 465 GLY G 598 REMARK 465 HIS G 599 REMARK 465 CYS G 600 REMARK 465 GLU G 601 REMARK 465 MET G 602 REMARK 465 CYS G 603 REMARK 465 SER G 604 REMARK 465 LEU G 605 REMARK 465 PRO G 606 REMARK 465 ARG G 607 REMARK 465 THR G 608 REMARK 465 MET I 1 REMARK 465 GLN I 2 REMARK 465 ILE I 3 REMARK 465 PHE I 4 REMARK 465 VAL I 5 REMARK 465 LYS I 6 REMARK 465 THR I 7 REMARK 465 LEU I 8 REMARK 465 THR I 9 REMARK 465 GLY I 10 REMARK 465 GLU I 51 REMARK 465 ASP I 52 REMARK 465 GLY I 53 REMARK 465 ARG I 54 REMARK 465 THR I 55 REMARK 465 LEU I 56 REMARK 465 SER I 57 REMARK 465 ASP I 58 REMARK 465 TYR I 59 REMARK 465 ASN I 60 REMARK 465 ILE I 61 REMARK 465 GLN I 62 REMARK 465 LYS I 63 REMARK 465 GLU I 64 REMARK 465 SER I 65 REMARK 465 THR I 66 REMARK 465 LEU I 67 REMARK 465 HIS I 68 REMARK 465 LEU I 69 REMARK 465 VAL I 70 REMARK 465 LEU I 71 REMARK 465 ARG I 72 REMARK 465 LEU I 73 REMARK 465 ARG I 74 REMARK 465 GLY I 75 REMARK 465 GLY I 76 REMARK 465 MET P 1 REMARK 465 PHE P 2 REMARK 465 SER P 3 REMARK 465 PHE P 4 REMARK 465 ASN P 5 REMARK 465 MET P 6 REMARK 465 PHE P 7 REMARK 465 ASP P 8 REMARK 465 HIS P 9 REMARK 465 PRO P 10 REMARK 465 ILE P 11 REMARK 465 PRO P 12 REMARK 465 ARG P 13 REMARK 465 VAL P 14 REMARK 465 PHE P 15 REMARK 465 GLN P 16 REMARK 465 ASN P 17 REMARK 465 ARG P 18 REMARK 465 PHE P 19 REMARK 465 SER P 20 REMARK 465 THR P 21 REMARK 465 GLN P 22 REMARK 465 TYR P 23 REMARK 465 ARG P 24 REMARK 465 CYS P 25 REMARK 465 PHE P 26 REMARK 465 SER P 27 REMARK 465 VAL P 28 REMARK 465 SER P 29 REMARK 465 MET P 30 REMARK 465 LEU P 31 REMARK 465 ALA P 32 REMARK 465 GLY P 33 REMARK 465 PRO P 34 REMARK 465 ASN P 35 REMARK 465 ASP P 36 REMARK 465 ARG P 37 REMARK 465 SER P 38 REMARK 465 ASP P 39 REMARK 465 VAL P 40 REMARK 465 GLU P 41 REMARK 465 LYS P 42 REMARK 465 GLY P 43 REMARK 465 GLY P 44 REMARK 465 LYS P 45 REMARK 465 ILE P 46 REMARK 465 ILE P 47 REMARK 465 MET P 48 REMARK 465 PRO P 49 REMARK 465 PRO P 50 REMARK 465 SER P 51 REMARK 465 ALA P 52 REMARK 465 LEU P 53 REMARK 465 ASP P 54 REMARK 465 GLN P 55 REMARK 465 LEU P 56 REMARK 465 SER P 57 REMARK 465 ARG P 58 REMARK 465 LEU P 59 REMARK 465 ASN P 60 REMARK 465 ILE P 61 REMARK 465 THR P 62 REMARK 465 TYR P 63 REMARK 465 PRO P 64 REMARK 465 MET P 65 REMARK 465 LEU P 66 REMARK 465 PHE P 67 REMARK 465 LYS P 68 REMARK 465 LEU P 69 REMARK 465 THR P 70 REMARK 465 ASN P 71 REMARK 465 LYS P 72 REMARK 465 ASN P 73 REMARK 465 SER P 74 REMARK 465 ASP P 75 REMARK 465 ARG P 76 REMARK 465 MET P 77 REMARK 465 THR P 78 REMARK 465 HIS P 79 REMARK 465 CYS P 80 REMARK 465 GLY P 81 REMARK 465 VAL P 82 REMARK 465 LEU P 83 REMARK 465 GLU P 84 REMARK 465 PHE P 85 REMARK 465 VAL P 86 REMARK 465 ALA P 87 REMARK 465 ASP P 88 REMARK 465 GLU P 89 REMARK 465 GLY P 90 REMARK 465 ILE P 91 REMARK 465 CYS P 92 REMARK 465 TYR P 93 REMARK 465 LEU P 94 REMARK 465 PRO P 95 REMARK 465 HIS P 96 REMARK 465 TRP P 97 REMARK 465 MET P 98 REMARK 465 MET P 99 REMARK 465 GLN P 100 REMARK 465 ASN P 101 REMARK 465 LEU P 102 REMARK 465 LEU P 103 REMARK 465 LEU P 104 REMARK 465 GLU P 105 REMARK 465 GLU P 106 REMARK 465 GLY P 107 REMARK 465 GLY P 108 REMARK 465 LEU P 109 REMARK 465 VAL P 110 REMARK 465 GLN P 111 REMARK 465 VAL P 112 REMARK 465 GLU P 113 REMARK 465 SER P 114 REMARK 465 VAL P 115 REMARK 465 ASN P 116 REMARK 465 LEU P 117 REMARK 465 GLN P 118 REMARK 465 VAL P 119 REMARK 465 ALA P 120 REMARK 465 THR P 121 REMARK 465 TYR P 122 REMARK 465 SER P 123 REMARK 465 LYS P 124 REMARK 465 PHE P 125 REMARK 465 GLN P 126 REMARK 465 PRO P 127 REMARK 465 GLN P 128 REMARK 465 SER P 129 REMARK 465 PRO P 130 REMARK 465 ASP P 131 REMARK 465 PHE P 132 REMARK 465 LEU P 133 REMARK 465 ASP P 134 REMARK 465 ILE P 135 REMARK 465 THR P 136 REMARK 465 ASN P 137 REMARK 465 PRO P 138 REMARK 465 LYS P 139 REMARK 465 ALA P 140 REMARK 465 VAL P 141 REMARK 465 LEU P 142 REMARK 465 GLU P 143 REMARK 465 ASN P 144 REMARK 465 ALA P 145 REMARK 465 LEU P 146 REMARK 465 ARG P 147 REMARK 465 ASN P 148 REMARK 465 PHE P 149 REMARK 465 ALA P 150 REMARK 465 CYS P 151 REMARK 465 LEU P 152 REMARK 465 THR P 153 REMARK 465 THR P 154 REMARK 465 GLY P 155 REMARK 465 ASP P 156 REMARK 465 VAL P 157 REMARK 465 ILE P 158 REMARK 465 ALA P 159 REMARK 465 ILE P 160 REMARK 465 ASN P 161 REMARK 465 TYR P 162 REMARK 465 ASN P 163 REMARK 465 GLU P 164 REMARK 465 LYS P 165 REMARK 465 ILE P 166 REMARK 465 TYR P 167 REMARK 465 GLU P 168 REMARK 465 LEU P 169 REMARK 465 ARG P 170 REMARK 465 VAL P 171 REMARK 465 MET P 172 REMARK 465 GLU P 173 REMARK 465 THR P 174 REMARK 465 LYS P 175 REMARK 465 PRO P 176 REMARK 465 ASP P 177 REMARK 465 LYS P 178 REMARK 465 ALA P 179 REMARK 465 VAL P 180 REMARK 465 SER P 181 REMARK 465 ILE P 182 REMARK 465 ILE P 183 REMARK 465 GLU P 184 REMARK 465 CYS P 185 REMARK 465 ASP P 186 REMARK 465 MET P 187 REMARK 465 ASN P 188 REMARK 465 VAL P 189 REMARK 465 ASP P 190 REMARK 465 PHE P 191 REMARK 465 ASP P 192 REMARK 465 ALA P 193 REMARK 465 PRO P 194 REMARK 465 LEU P 195 REMARK 465 GLY P 196 REMARK 465 TYR P 197 REMARK 465 LYS P 198 REMARK 465 GLU P 199 REMARK 465 PRO P 200 REMARK 465 GLU P 201 REMARK 465 ARG P 202 REMARK 465 GLN P 203 REMARK 465 VAL P 204 REMARK 465 GLN P 205 REMARK 465 HIS P 206 REMARK 465 GLU P 207 REMARK 465 GLU P 208 REMARK 465 SER P 209 REMARK 465 THR P 210 REMARK 465 GLU P 211 REMARK 465 GLY P 212 REMARK 465 GLU P 213 REMARK 465 ALA P 214 REMARK 465 ASP P 215 REMARK 465 HIS P 216 REMARK 465 SER P 217 REMARK 465 GLY P 218 REMARK 465 TYR P 219 REMARK 465 ALA P 220 REMARK 465 GLY P 221 REMARK 465 GLU P 222 REMARK 465 LEU P 223 REMARK 465 GLY P 224 REMARK 465 PHE P 225 REMARK 465 ARG P 226 REMARK 465 ALA P 227 REMARK 465 PHE P 228 REMARK 465 SER P 229 REMARK 465 GLY P 230 REMARK 465 SER P 231 REMARK 465 GLY P 232 REMARK 465 ASN P 233 REMARK 465 ARG P 234 REMARK 465 LEU P 235 REMARK 465 ASP P 236 REMARK 465 GLY P 237 REMARK 465 LYS P 238 REMARK 465 LYS P 239 REMARK 465 LYS P 240 REMARK 465 GLY P 241 REMARK 465 VAL P 242 REMARK 465 GLU P 243 REMARK 465 PRO P 244 REMARK 465 SER P 245 REMARK 465 PRO P 246 REMARK 465 SER P 247 REMARK 465 VAL P 278 REMARK 465 LYS P 279 REMARK 465 LYS P 280 REMARK 465 VAL P 281 REMARK 465 GLU P 282 REMARK 465 GLU P 283 REMARK 465 ASP P 284 REMARK 465 GLU P 285 REMARK 465 ALA P 286 REMARK 465 GLY P 287 REMARK 465 GLY P 288 REMARK 465 ARG P 289 REMARK 465 PHE P 290 REMARK 465 VAL P 291 REMARK 465 ALA P 292 REMARK 465 PHE P 293 REMARK 465 SER P 294 REMARK 465 GLY P 295 REMARK 465 GLU P 296 REMARK 465 GLY P 297 REMARK 465 GLN P 298 REMARK 465 SER P 299 REMARK 465 LEU P 300 REMARK 465 ARG P 301 REMARK 465 LYS P 302 REMARK 465 LYS P 303 REMARK 465 GLY P 304 REMARK 465 ARG P 305 REMARK 465 LYS P 306 REMARK 465 PRO P 307 REMARK 465 HIS P 308 REMARK 465 HIS P 309 REMARK 465 HIS P 310 REMARK 465 HIS P 311 REMARK 465 HIS P 312 REMARK 465 HIS P 313 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU G 129 -72.40 -101.83 REMARK 500 CYS G 130 58.81 32.43 REMARK 500 ASN G 202 33.92 -96.75 REMARK 500 HIS G 231 49.09 -85.11 REMARK 500 TYR G 334 173.75 179.92 REMARK 500 GLU G 398 29.77 46.75 REMARK 500 ALA G 440 51.78 -91.71 REMARK 500 GLU G 446 5.51 -68.74 REMARK 500 ASN G 469 66.11 -116.65 REMARK 500 MET G 519 87.81 -157.15 REMARK 500 THR H 7 -168.56 -78.58 REMARK 500 ILE H 44 62.48 38.92 REMARK 500 PHE H 45 -102.40 -152.60 REMARK 500 ALA H 46 -107.61 43.83 REMARK 500 TYR H 59 55.89 -96.93 REMARK 500 ASP I 39 26.02 46.25 REMARK 500 PHE I 45 178.07 61.65 REMARK 500 ALA I 46 146.65 -172.28 REMARK 500 ASN J 60 60.64 61.00 REMARK 500 ARG J 74 -116.60 35.19 REMARK 500 GLN K 40 41.69 -104.69 REMARK 500 VAL K 70 -67.75 -124.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN G 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS G 130 SG REMARK 620 2 HIS G 132 NE2 74.2 REMARK 620 3 CYS G 138 SG 114.9 63.5 REMARK 620 4 CYS G 141 SG 115.7 170.1 110.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN G 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS G 194 SG REMARK 620 2 HIS G 197 NE2 134.6 REMARK 620 3 CYS G 205 SG 115.2 84.3 REMARK 620 4 CYS G 208 SG 113.8 94.4 110.1 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9YW2 RELATED DB: PDB REMARK 900 RELATED ID: EMD-73536 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-76026 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SUBSTRATE ENGAGED P97-UFD1-NPL4-FAF1 COMPLEX REMARK 900 (NPL4 FOCUSED) DBREF 11SY G 2 608 UNP Q8TAT6 NPL4_HUMAN 2 608 DBREF 11SY H 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 11SY I 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 11SY J 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 11SY K 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 11SY P 1 307 UNP Q92890 UFD1_HUMAN 1 307 SEQADV 11SY MET G -2 UNP Q8TAT6 INITIATING METHIONINE SEQADV 11SY GLY G -1 UNP Q8TAT6 EXPRESSION TAG SEQADV 11SY GLY G 0 UNP Q8TAT6 EXPRESSION TAG SEQADV 11SY GLY G 1 UNP Q8TAT6 EXPRESSION TAG SEQADV 11SY HIS P 308 UNP Q92890 EXPRESSION TAG SEQADV 11SY HIS P 309 UNP Q92890 EXPRESSION TAG SEQADV 11SY HIS P 310 UNP Q92890 EXPRESSION TAG SEQADV 11SY HIS P 311 UNP Q92890 EXPRESSION TAG SEQADV 11SY HIS P 312 UNP Q92890 EXPRESSION TAG SEQADV 11SY HIS P 313 UNP Q92890 EXPRESSION TAG SEQRES 1 G 611 MET GLY GLY GLY ALA GLU SER ILE ILE ILE ARG VAL GLN SEQRES 2 G 611 SER PRO ASP GLY VAL LYS ARG ILE THR ALA THR LYS ARG SEQRES 3 G 611 GLU THR ALA ALA THR PHE LEU LYS LYS VAL ALA LYS GLU SEQRES 4 G 611 PHE GLY PHE GLN ASN ASN GLY PHE SER VAL TYR ILE ASN SEQRES 5 G 611 ARG ASN LYS THR GLY GLU ILE THR ALA SER SER ASN LYS SEQRES 6 G 611 SER LEU ASN LEU LEU LYS ILE LYS HIS GLY ASP LEU LEU SEQRES 7 G 611 PHE LEU PHE PRO SER SER LEU ALA GLY PRO SER SER GLU SEQRES 8 G 611 MET GLU THR SER VAL PRO PRO GLY PHE LYS VAL PHE GLY SEQRES 9 G 611 ALA PRO ASN VAL VAL GLU ASP GLU ILE ASP GLN TYR LEU SEQRES 10 G 611 SER LYS GLN ASP GLY LYS ILE TYR ARG SER ARG ASP PRO SEQRES 11 G 611 GLN LEU CYS ARG HIS GLY PRO LEU GLY LYS CYS VAL HIS SEQRES 12 G 611 CYS VAL PRO LEU GLU PRO PHE ASP GLU ASP TYR LEU ASN SEQRES 13 G 611 HIS LEU GLU PRO PRO VAL LYS HIS MET SER PHE HIS ALA SEQRES 14 G 611 TYR ILE ARG LYS LEU THR GLY GLY ALA ASP LYS GLY LYS SEQRES 15 G 611 PHE VAL ALA LEU GLU ASN ILE SER CYS LYS ILE LYS SER SEQRES 16 G 611 GLY CYS GLU GLY HIS LEU PRO TRP PRO ASN GLY ILE CYS SEQRES 17 G 611 THR LYS CYS GLN PRO SER ALA ILE THR LEU ASN ARG GLN SEQRES 18 G 611 LYS TYR ARG HIS VAL ASP ASN ILE MET PHE GLU ASN HIS SEQRES 19 G 611 THR VAL ALA ASP ARG PHE LEU ASP PHE TRP ARG LYS THR SEQRES 20 G 611 GLY ASN GLN HIS PHE GLY TYR LEU TYR GLY ARG TYR THR SEQRES 21 G 611 GLU HIS LYS ASP ILE PRO LEU GLY ILE ARG ALA GLU VAL SEQRES 22 G 611 ALA ALA ILE TYR GLU PRO PRO GLN ILE GLY THR GLN ASN SEQRES 23 G 611 SER LEU GLU LEU LEU GLU ASP PRO LYS ALA GLU VAL VAL SEQRES 24 G 611 ASP GLU ILE ALA ALA LYS LEU GLY LEU ARG LYS VAL GLY SEQRES 25 G 611 TRP ILE PHE THR ASP LEU VAL SER GLU ASP THR ARG LYS SEQRES 26 G 611 GLY THR VAL ARG TYR SER ARG ASN LYS ASP THR TYR PHE SEQRES 27 G 611 LEU SER SER GLU GLU CYS ILE THR ALA GLY ASP PHE GLN SEQRES 28 G 611 ASN LYS HIS PRO ASN MET CYS ARG LEU SER PRO ASP GLY SEQRES 29 G 611 HIS PHE GLY SER LYS PHE VAL THR ALA VAL ALA THR GLY SEQRES 30 G 611 GLY PRO ASP ASN GLN VAL HIS PHE GLU GLY TYR GLN VAL SEQRES 31 G 611 SER ASN GLN CYS MET ALA LEU VAL ARG ASP GLU CYS LEU SEQRES 32 G 611 LEU PRO CYS LYS ASP ALA PRO GLU LEU GLY TYR ALA LYS SEQRES 33 G 611 GLU SER SER SER GLU GLN TYR VAL PRO ASP VAL PHE TYR SEQRES 34 G 611 LYS ASP VAL ASP LYS PHE GLY ASN GLU ILE THR GLN LEU SEQRES 35 G 611 ALA ARG PRO LEU PRO VAL GLU TYR LEU ILE ILE ASP ILE SEQRES 36 G 611 THR THR THR PHE PRO LYS ASP PRO VAL TYR THR PHE SER SEQRES 37 G 611 ILE SER GLN ASN PRO PHE PRO ILE GLU ASN ARG ASP VAL SEQRES 38 G 611 LEU GLY GLU THR GLN ASP PHE HIS SER LEU ALA THR TYR SEQRES 39 G 611 LEU SER GLN ASN THR SER SER VAL PHE LEU ASP THR ILE SEQRES 40 G 611 SER ASP PHE HIS LEU LEU LEU PHE LEU VAL THR ASN GLU SEQRES 41 G 611 VAL MET PRO LEU GLN ASP SER ILE SER LEU LEU LEU GLU SEQRES 42 G 611 ALA VAL ARG THR ARG ASN GLU GLU LEU ALA GLN THR TRP SEQRES 43 G 611 LYS ARG SER GLU GLN TRP ALA THR ILE GLU GLN LEU CYS SEQRES 44 G 611 SER THR VAL GLY GLY GLN LEU PRO GLY LEU HIS GLU TYR SEQRES 45 G 611 GLY ALA VAL GLY GLY SER THR HIS THR ALA THR ALA ALA SEQRES 46 G 611 MET TRP ALA CYS GLN HIS CYS THR PHE MET ASN GLN PRO SEQRES 47 G 611 GLY THR GLY HIS CYS GLU MET CYS SER LEU PRO ARG THR SEQRES 1 H 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 H 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 H 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 H 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 H 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 H 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 I 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 I 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 I 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 I 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 I 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 I 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 J 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 J 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 J 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 J 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 J 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 J 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 K 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 K 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 K 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 K 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 K 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 K 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 P 313 MET PHE SER PHE ASN MET PHE ASP HIS PRO ILE PRO ARG SEQRES 2 P 313 VAL PHE GLN ASN ARG PHE SER THR GLN TYR ARG CYS PHE SEQRES 3 P 313 SER VAL SER MET LEU ALA GLY PRO ASN ASP ARG SER ASP SEQRES 4 P 313 VAL GLU LYS GLY GLY LYS ILE ILE MET PRO PRO SER ALA SEQRES 5 P 313 LEU ASP GLN LEU SER ARG LEU ASN ILE THR TYR PRO MET SEQRES 6 P 313 LEU PHE LYS LEU THR ASN LYS ASN SER ASP ARG MET THR SEQRES 7 P 313 HIS CYS GLY VAL LEU GLU PHE VAL ALA ASP GLU GLY ILE SEQRES 8 P 313 CYS TYR LEU PRO HIS TRP MET MET GLN ASN LEU LEU LEU SEQRES 9 P 313 GLU GLU GLY GLY LEU VAL GLN VAL GLU SER VAL ASN LEU SEQRES 10 P 313 GLN VAL ALA THR TYR SER LYS PHE GLN PRO GLN SER PRO SEQRES 11 P 313 ASP PHE LEU ASP ILE THR ASN PRO LYS ALA VAL LEU GLU SEQRES 12 P 313 ASN ALA LEU ARG ASN PHE ALA CYS LEU THR THR GLY ASP SEQRES 13 P 313 VAL ILE ALA ILE ASN TYR ASN GLU LYS ILE TYR GLU LEU SEQRES 14 P 313 ARG VAL MET GLU THR LYS PRO ASP LYS ALA VAL SER ILE SEQRES 15 P 313 ILE GLU CYS ASP MET ASN VAL ASP PHE ASP ALA PRO LEU SEQRES 16 P 313 GLY TYR LYS GLU PRO GLU ARG GLN VAL GLN HIS GLU GLU SEQRES 17 P 313 SER THR GLU GLY GLU ALA ASP HIS SER GLY TYR ALA GLY SEQRES 18 P 313 GLU LEU GLY PHE ARG ALA PHE SER GLY SER GLY ASN ARG SEQRES 19 P 313 LEU ASP GLY LYS LYS LYS GLY VAL GLU PRO SER PRO SER SEQRES 20 P 313 PRO ILE LYS PRO GLY ASP ILE LYS ARG GLY ILE PRO ASN SEQRES 21 P 313 TYR GLU PHE LYS LEU GLY LYS ILE THR PHE ILE ARG ASN SEQRES 22 P 313 SER ARG PRO LEU VAL LYS LYS VAL GLU GLU ASP GLU ALA SEQRES 23 P 313 GLY GLY ARG PHE VAL ALA PHE SER GLY GLU GLY GLN SER SEQRES 24 P 313 LEU ARG LYS LYS GLY ARG LYS PRO HIS HIS HIS HIS HIS SEQRES 25 P 313 HIS HET ZN G 701 1 HET ZN G 702 1 HETNAM ZN ZINC ION FORMUL 7 ZN 2(ZN 2+) HELIX 1 AA1 ASP G 108 LYS G 116 1 9 HELIX 2 AA2 ASP G 148 ASN G 153 1 6 HELIX 3 AA3 PHE G 164 GLY G 173 1 10 HELIX 4 AA4 THR G 232 GLY G 245 1 14 HELIX 5 AA5 LYS G 292 LEU G 303 1 12 HELIX 6 AA6 SER G 337 HIS G 351 1 15 HELIX 7 AA7 SER G 388 ASP G 397 1 10 HELIX 8 AA8 ASP G 484 ASN G 495 1 12 HELIX 9 AA9 PHE G 500 SER G 505 1 6 HELIX 10 AB1 ASP G 506 ASN G 516 1 11 HELIX 11 AB2 SER G 524 ARG G 535 1 12 HELIX 12 AB3 ASN G 536 ARG G 545 1 10 HELIX 13 AB4 SER G 546 THR G 558 1 13 HELIX 14 AB5 THR H 22 GLY H 35 1 14 HELIX 15 AB6 PRO H 37 GLN H 41 5 5 HELIX 16 AB7 THR I 22 GLN I 31 1 10 HELIX 17 AB8 THR J 22 GLY J 35 1 14 HELIX 18 AB9 THR K 22 GLU K 34 1 13 HELIX 19 AC1 PRO K 37 GLN K 41 5 5 SHEET 1 AA1 2 MET G 162 SER G 163 0 SHEET 2 AA1 2 TYR G 220 ARG G 221 1 O ARG G 221 N MET G 162 SHEET 1 AA2 3 ILE G 213 THR G 214 0 SHEET 2 AA2 3 VAL G 424 VAL G 429 1 O PHE G 425 N ILE G 213 SHEET 3 AA2 3 GLU G 435 LEU G 439 -1 O ILE G 436 N ASP G 428 SHEET 1 AA3 9 GLN I 40 GLN I 41 0 SHEET 2 AA3 9 ILE G 449 PRO G 457 -1 N PHE G 456 O GLN I 41 SHEET 3 AA3 9 VAL G 380 VAL G 387 -1 N GLY G 384 O ILE G 452 SHEET 4 AA3 9 VAL G 368 GLY G 374 -1 N THR G 369 O TYR G 385 SHEET 5 AA3 9 ARG G 306 THR G 313 1 N TRP G 310 O ALA G 370 SHEET 6 AA3 9 PHE G 249 HIS G 259 -1 N GLY G 254 O ARG G 306 SHEET 7 AA3 9 GLY G 265 TYR G 274 -1 O ARG G 267 N THR G 257 SHEET 8 AA3 9 ASN G 225 PHE G 228 1 N MET G 227 O ALA G 268 SHEET 9 AA3 9 ILE G 449 PRO G 457 1 O THR G 455 N ILE G 226 SHEET 1 AA4 2 SER G 284 LEU G 285 0 SHEET 2 AA4 2 ILE P 268 THR P 269 -1 O ILE P 268 N LEU G 285 SHEET 1 AA5 2 PRO G 352 MET G 354 0 SHEET 2 AA5 2 HIS G 362 SER G 365 -1 O PHE G 363 N ASN G 353 SHEET 1 AA6 3 LEU G 400 PRO G 402 0 SHEET 2 AA6 3 LEU G 409 ALA G 412 -1 O TYR G 411 N LEU G 401 SHEET 3 AA6 3 PRO G 442 PRO G 444 -1 O LEU G 443 N GLY G 410 SHEET 1 AA7 3 THR H 12 GLU H 16 0 SHEET 2 AA7 3 GLN H 2 LYS H 6 -1 N ILE H 3 O LEU H 15 SHEET 3 AA7 3 LEU H 67 HIS H 68 1 O LEU H 67 N PHE H 4 SHEET 1 AA8 2 GLN J 2 ILE J 3 0 SHEET 2 AA8 2 LEU J 15 GLU J 16 -1 O LEU J 15 N ILE J 3 SHEET 1 AA9 2 VAL J 5 LYS J 6 0 SHEET 2 AA9 2 LEU J 67 HIS J 68 1 O LEU J 67 N LYS J 6 SHEET 1 AB1 2 ILE J 44 PHE J 45 0 SHEET 2 AB1 2 LYS J 48 GLN J 49 -1 O LYS J 48 N PHE J 45 SHEET 1 AB2 4 THR K 12 GLU K 16 0 SHEET 2 AB2 4 GLN K 2 LYS K 6 -1 N ILE K 3 O LEU K 15 SHEET 3 AB2 4 THR K 66 LEU K 69 1 O LEU K 69 N LYS K 6 SHEET 4 AB2 4 LEU K 43 PHE K 45 -1 N ILE K 44 O HIS K 68 LINK SG CYS G 130 ZN ZN G 701 1555 1555 2.33 LINK NE2 HIS G 132 ZN ZN G 701 1555 1555 2.05 LINK SG CYS G 138 ZN ZN G 701 1555 1555 2.32 LINK SG CYS G 141 ZN ZN G 701 1555 1555 2.32 LINK SG CYS G 194 ZN ZN G 702 1555 1555 2.32 LINK NE2 HIS G 197 ZN ZN G 702 1555 1555 2.04 LINK SG CYS G 205 ZN ZN G 702 1555 1555 2.31 LINK SG CYS G 208 ZN ZN G 702 1555 1555 2.31 CISPEP 1 GLU G 156 PRO G 157 0 -0.65 CISPEP 2 TRP G 200 PRO G 201 0 -2.55 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 CONECT 216 6023 CONECT 237 6023 CONECT 275 6023 CONECT 298 6023 CONECT 715 6024 CONECT 738 6024 CONECT 800 6024 CONECT 822 6024 CONECT 6023 216 237 275 298 CONECT 6024 715 738 800 822 MASTER 647 0 2 19 34 0 0 6 6018 6 10 96 END