HEADER PROTEIN BINDING 13-AUG-24 9D5A TITLE STRUCTURE OF CITROBACTER MULTI-UBIQUITIN PROTEIN, LOCAL REFINEMENT OF TITLE 2 ONE FULL-LENGTH PROTOMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTI-UBIQUITIN DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CITROBACTER SP. RHBSTW-00271; SOURCE 3 ORGANISM_TAXID: 2742642; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS FILAMENT, BETA-GRASP, PROTEIN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR M.GONG,Y.GU,K.D.CORBETT REVDAT 3 18-JUN-25 9D5A 1 JRNL REVDAT 2 30-APR-25 9D5A 1 JRNL REVDAT 1 02-APR-25 9D5A 0 JRNL AUTH M.GONG,Q.YE,Y.GU,L.R.CHAMBERS,A.A.BOBKOV,N.K.ARAKAWA, JRNL AUTH 2 M.MATYSZEWSKI,K.D.CORBETT JRNL TITL STRUCTURAL DIVERSITY AND OLIGOMERIZATION OF BACTERIAL JRNL TITL 2 UBIQUITIN-LIKE PROTEINS. JRNL REF STRUCTURE V. 33 1016 2025 JRNL REFN ISSN 0969-2126 JRNL PMID 40250427 JRNL DOI 10.1016/J.STR.2025.03.011 REMARK 2 REMARK 2 RESOLUTION. 2.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE 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) : 2.730 REMARK 3 NUMBER OF PARTICLES : 148697 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 9D5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000287311. 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 : FILAMENT REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : FILAMENT ASSEMBLY OF REMARK 245 CITROBACTER SP. UBIQUITIN-LIKE REMARK 245 (UBL) PROTEIN WITH CA ION 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 : 8.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 4500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 A -17 REMARK 465 LYS A -16 REMARK 465 SER A -15 REMARK 465 SER A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 SER A -1 REMARK 465 ASN A 0 REMARK 465 ALA A 1 REMARK 465 GLN A 2 REMARK 465 ASP A 3 REMARK 465 ILE A 4 REMARK 465 GLN A 5 REMARK 465 SER A 6 REMARK 465 GLN A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 ARG A 11 REMARK 465 LYS A 224 REMARK 465 ASP A 225 REMARK 465 VAL A 226 REMARK 465 ASN A 227 REMARK 465 ASN A 228 REMARK 465 GLY A 229 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 CA A 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 30 OD2 REMARK 620 2 THR A 32 O 78.2 REMARK 620 3 THR A 32 OG1 105.4 61.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 62 OE2 REMARK 620 2 ASP A 63 O 87.8 REMARK 620 3 GLU A 68 OE1 141.1 80.0 REMARK 620 4 GLU A 68 OE2 100.2 103.2 48.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 125 O REMARK 620 2 ASP A 130 OD1 89.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 141 O REMARK 620 2 GLY A 143 O 86.2 REMARK 620 3 GLY A 145 O 164.9 82.3 REMARK 620 4 GLU A 147 OE1 98.3 125.7 80.9 REMARK 620 5 GLU A 147 OE2 82.1 72.1 85.2 55.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 211 O REMARK 620 2 THR A 213 O 78.8 REMARK 620 3 GLY A 215 O 155.9 78.8 REMARK 620 4 GLU A 217 OE1 101.9 110.6 78.1 REMARK 620 5 GLU A 217 OE2 71.6 75.0 94.2 43.2 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-46577 RELATED DB: EMDB REMARK 900 STRUCTURE OF CITROBACTER MULTI-UBIQUITIN PROTEIN, LOCAL REFINEMENT REMARK 900 OF ONE FULL-LENGTH PROTOMER DBREF 9D5A A -17 229 PDB 9D5A 9D5A -17 229 SEQRES 1 A 247 MET LYS SER SER HIS HIS HIS HIS HIS HIS GLU ASN LEU SEQRES 2 A 247 TYR PHE GLN SER ASN ALA GLN ASP ILE GLN SER GLN HIS SEQRES 3 A 247 HIS HIS ARG ARG PHE ILE GLU VAL ALA ASP GLU THR LEU SEQRES 4 A 247 SER PHE ARG GLN VAL VAL MET GLU ASP SER THR PRO ASN SEQRES 5 A 247 GLY SER GLN ILE SER ALA ALA SER GLY PHE LYS PRO ASP SEQRES 6 A 247 GLN MET PRO VAL VAL LEU MET LEU LEU PRO ASN GLY SER SEQRES 7 A 247 LEU GLU ASP ILE ARG PRO ASP GLU VAL VAL ASP LEU SER SEQRES 8 A 247 SER GLU VAL ARG ARG PHE ILE VAL VAL GLU SER ASP ARG SEQRES 9 A 247 THR TYR PHE PHE THR ILE ASP GLY ALA ARG LEU GLU TRP SEQRES 10 A 247 PRO CYS ARG PHE ILE THR GLY TYR SER ILE ARG GLN LEU SEQRES 11 A 247 GLY ASP ILE GLY ASP ASN LYS LYS LEU LEU LEU GLU ARG SEQRES 12 A 247 GLU ASP GLU ALA ASP LEU GLU VAL GLN ASN ASP GLN ILE SEQRES 13 A 247 ILE ASP LEU ASP GLY ASP GLY ILE GLU ARG PHE ILE SER SEQRES 14 A 247 ARG LYS ALA THR TRP LYS LEU ASN ILE GLN GLY LYS GLU SEQRES 15 A 247 PHE THR PHE ASP THR PRO THR VAL VAL ILE ARG ASP ALA SEQRES 16 A 247 VAL ILE ARG ALA GLY LEU ASN PRO ASN GLN ALA TRP HIS SEQRES 17 A 247 ILE PHE LEU LYS VAL GLU GLY GLN PRO LYS VAL GLU LYS SEQRES 18 A 247 ASN ILE ASP ASP VAL ILE ASP LEU ARG THR PRO GLY ILE SEQRES 19 A 247 GLU LYS LEU ARG LEU THR PRO LYS ASP VAL ASN ASN GLY HET CA A 301 1 HET CA A 302 1 HET CA A 303 1 HET CA A 304 1 HET CA A 305 1 HETNAM CA CALCIUM ION FORMUL 2 CA 5(CA 2+) HELIX 1 AA1 ASN A 34 SER A 42 1 9 HELIX 2 AA2 GLY A 106 ASP A 114 1 9 HELIX 3 AA3 ILE A 174 GLY A 182 1 9 SHEET 1 AA1 5 ARG A 24 VAL A 27 0 SHEET 2 AA1 5 PHE A 13 ALA A 17 -1 N ILE A 14 O VAL A 26 SHEET 3 AA1 5 ARG A 78 VAL A 82 1 O VAL A 81 N ALA A 17 SHEET 4 AA1 5 VAL A 51 LEU A 55 -1 N LEU A 55 O ARG A 78 SHEET 5 AA1 5 LEU A 61 ASP A 63 -1 O GLU A 62 N MET A 54 SHEET 1 AA2 5 ALA A 95 TRP A 99 0 SHEET 2 AA2 5 TYR A 88 ILE A 92 -1 N PHE A 90 O LEU A 97 SHEET 3 AA2 5 GLU A 147 LYS A 153 1 O PHE A 149 N THR A 91 SHEET 4 AA2 5 LYS A 119 LEU A 123 -1 N LYS A 120 O ARG A 152 SHEET 5 AA2 5 LEU A 131 GLU A 132 -1 O LEU A 131 N LEU A 123 SHEET 1 AA3 2 PHE A 103 THR A 105 0 SHEET 2 AA3 2 ILE A 138 ASP A 140 -1 O ILE A 139 N ILE A 104 SHEET 1 AA4 5 LYS A 163 PHE A 167 0 SHEET 2 AA4 5 TRP A 156 ILE A 160 -1 N LEU A 158 O PHE A 165 SHEET 3 AA4 5 GLU A 217 THR A 222 1 O GLU A 217 N ASN A 159 SHEET 4 AA4 5 HIS A 190 LYS A 194 -1 N HIS A 190 O THR A 222 SHEET 5 AA4 5 VAL A 201 LYS A 203 -1 O VAL A 201 N LEU A 193 SHEET 1 AA5 2 THR A 171 VAL A 173 0 SHEET 2 AA5 2 VAL A 208 ASP A 210 -1 O ILE A 209 N VAL A 172 LINK OD2 ASP A 30 CA CA A 303 1555 1555 2.34 LINK O THR A 32 CA CA A 303 1555 1555 2.37 LINK OG1 THR A 32 CA CA A 303 1555 1555 2.60 LINK OE2 GLU A 62 CA CA A 302 1555 1555 3.01 LINK O ASP A 63 CA CA A 302 1555 1555 2.38 LINK OE1 GLU A 68 CA CA A 302 1555 1555 2.44 LINK OE2 GLU A 68 CA CA A 302 1555 1555 2.82 LINK O ARG A 125 CA CA A 304 1555 1555 2.40 LINK OD1 ASP A 130 CA CA A 304 1555 1555 2.48 LINK O LEU A 141 CA CA A 301 1555 1555 2.39 LINK O GLY A 143 CA CA A 301 1555 1555 2.52 LINK O GLY A 145 CA CA A 301 1555 1555 2.48 LINK OE1 GLU A 147 CA CA A 301 1555 1555 2.33 LINK OE2 GLU A 147 CA CA A 301 1555 1555 2.37 LINK O LEU A 211 CA CA A 305 1555 1555 2.31 LINK O THR A 213 CA CA A 305 1555 1555 2.74 LINK O GLY A 215 CA CA A 305 1555 1555 2.31 LINK OE1 GLU A 217 CA CA A 305 1555 1555 2.82 LINK OE2 GLU A 217 CA CA A 305 1555 1555 3.08 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 TER 1700 PRO A 223 HETATM 1701 CA CA A 301 172.862 179.685 130.088 1.00105.70 CA HETATM 1702 CA CA A 302 157.508 166.939 136.193 1.00117.45 CA HETATM 1703 CA CA A 303 149.412 160.548 148.556 1.00101.87 CA HETATM 1704 CA CA A 304 185.131 174.366 120.763 1.00105.09 CA HETATM 1705 CA CA A 305 197.864 173.956 129.030 1.00119.62 CA CONECT 159 1703 CONECT 169 1703 CONECT 171 1703 CONECT 387 1702 CONECT 391 1702 CONECT 437 1702 CONECT 438 1702 CONECT 903 1704 CONECT 948 1704 CONECT 1035 1701 CONECT 1051 1701 CONECT 1063 1701 CONECT 1079 1701 CONECT 1080 1701 CONECT 1599 1705 CONECT 1618 1705 CONECT 1632 1705 CONECT 1648 1705 CONECT 1649 1705 CONECT 1701 1035 1051 1063 1079 CONECT 1701 1080 CONECT 1702 387 391 437 438 CONECT 1703 159 169 171 CONECT 1704 903 948 CONECT 1705 1599 1618 1632 1648 CONECT 1705 1649 MASTER 190 0 5 3 19 0 0 6 1704 1 26 19 END