HEADER LIGASE/IMMUNE SYSTEM 15-APR-25 9O7G TITLE CHIP E3 LIGASE U-BOX-FAB H1 EPITOPE FOCUSED REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: H1 FAB LIGHT CHAIN; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE CHIP; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: ANTIGEN NY-CO-7,CLL-ASSOCIATED ANTIGEN KW-8,CARBOXY TERMINUS COMPND 9 OF HSP70-INTERACTING PROTEIN,RING-TYPE E3 UBIQUITIN TRANSFERASE CHIP, COMPND 10 STIP1 HOMOLOGY AND U BOX-CONTAINING PROTEIN 1; COMPND 11 EC: 2.3.2.27; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: H1 FAB HEAVY CHAIN; COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: STUB1, CHIP, PP1131; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS U-BOX E3 LIGASE, FAB, CRYO-EM, PROTEIN DEGRADATION, LIGASE-IMMUNE KEYWDS 2 SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR A.UNNIKRISHNAN,D.SOUTHWORTH REVDAT 1 13-MAY-26 9O7G 0 JRNL AUTH A.UNNIKRISHNAN,D.SOUTHWORTH JRNL TITL STRUCTURES OF FAB-STABILIZED CHIP REVEAL A CONFORMATIONAL JRNL TITL 2 SWITCH IMPORTANT IN E3 LIGASE AND CHAPERONE FUNCTIONS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 482143 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 9O7G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-APR-25. REMARK 100 THE DEPOSITION ID IS D_1000295019. 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 : FAB H1-CHIP E3 LIGASE U-BOX REMARK 245 EPITOPE 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 : 7.40 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6600.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, B, D 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 GLY B 298 REMARK 465 TRP B 299 REMARK 465 VAL B 300 REMARK 465 GLU B 301 REMARK 465 ASP B 302 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 263 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG D 70 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 GLN C 10 147.97 57.83 REMARK 500 THR C 32 78.42 -67.43 REMARK 500 ASN C 110 96.83 64.17 REMARK 500 LEU B 239 118.39 57.43 REMARK 500 ALA B 292 24.73 -77.71 REMARK 500 ASN D 43 -38.46 61.31 REMARK 500 ASN D 67 -37.41 64.30 REMARK 500 ASN D 68 -4.99 -148.01 REMARK 500 SER D 109 -101.32 -84.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70198 RELATED DB: EMDB REMARK 900 CHIP E3 LIGASE U-BOX-FAB H1 EPITOPE FOCUSED REFINEMENT DBREF 9O7G C 6 126 PDB 9O7G 9O7G 6 126 DBREF 9O7G B 226 302 UNP Q9UNE7 CHIP_HUMAN 226 302 DBREF 9O7G D 17 126 PDB 9O7G 9O7G 17 126 SEQRES 1 C 121 VAL GLN LEU VAL GLN SER GLY SER GLU VAL LYS LYS PRO SEQRES 2 C 121 GLY ALA SER VAL LYS VAL SER CYS LYS ALA SER GLY TYR SEQRES 3 C 121 THR PHE THR ASN TYR GLY ILE SER TRP VAL ARG GLN ALA SEQRES 4 C 121 PRO GLY GLN GLY LEU GLU TRP MET GLY TRP ILE SER ALA SEQRES 5 C 121 TYR ASN GLY ASN THR ASN TYR ALA GLN ASN PHE GLN GLY SEQRES 6 C 121 ARG VAL THR MET THR THR ASP THR SER THR LYS THR ALA SEQRES 7 C 121 TYR MET GLU LEU ARG SER LEU ARG SER ASP ASP THR ALA SEQRES 8 C 121 VAL TYR PHE CYS ALA ARG SER GLY TYR SER GLY TYR ASP SEQRES 9 C 121 ASN ASN LEU GLY ALA PHE ASP ILE TRP GLY GLN GLY THR SEQRES 10 C 121 MET VAL THR VAL SEQRES 1 B 77 ASP ILE PRO ASP TYR LEU CYS GLY LYS ILE SER PHE GLU SEQRES 2 B 77 LEU MET ARG GLU PRO CYS ILE THR PRO SER GLY ILE THR SEQRES 3 B 77 TYR ASP ARG LYS ASP ILE GLU GLU HIS LEU GLN ARG VAL SEQRES 4 B 77 GLY HIS PHE ASP PRO VAL THR ARG SER PRO LEU THR GLN SEQRES 5 B 77 GLU GLN LEU ILE PRO ASN LEU ALA MET LYS GLU VAL ILE SEQRES 6 B 77 ASP ALA PHE ILE SER GLU ASN GLY TRP VAL GLU ASP SEQRES 1 D 110 SER VAL VAL THR GLN PRO PRO SER VAL SER ALA ALA PRO SEQRES 2 D 110 GLY GLN LYS VAL THR ILE SER CYS SER GLY THR SER SER SEQRES 3 D 110 ASN ILE GLY ASN SER TYR VAL THR TRP TYR GLN GLN LEU SEQRES 4 D 110 PRO GLY ALA ALA PRO LYS LEU LEU ILE TYR ASP ASN ASN SEQRES 5 D 110 LYS ARG PRO SER GLY ILE PRO ASP ARG PHE SER GLY SER SEQRES 6 D 110 LYS SER GLY THR SER ALA THR LEU GLY ILE THR GLY LEU SEQRES 7 D 110 GLN THR GLY ASP GLU ALA ASP TYR TYR CYS ALA THR TRP SEQRES 8 D 110 ASP SER SER LEU THR ALA GLY ARG VAL PHE GLY GLY GLY SEQRES 9 D 110 THR ARG LEU THR VAL LEU HELIX 1 AA1 THR C 32 THR C 34 5 3 HELIX 2 AA2 ARG C 91 THR C 95 5 5 HELIX 3 AA3 PRO B 228 CYS B 232 5 5 HELIX 4 AA4 ARG B 254 VAL B 264 1 11 HELIX 5 AA5 ASN B 283 SER B 295 1 13 HELIX 6 AA6 GLN D 95 GLU D 99 5 5 SHEET 1 AA1 6 GLU C 14 VAL C 15 0 SHEET 2 AA1 6 THR C 122 THR C 125 1 O MET C 123 N GLU C 14 SHEET 3 AA1 6 ALA C 96 TYR C 105 -1 N ALA C 96 O VAL C 124 SHEET 4 AA1 6 TYR C 36 GLN C 43 -1 N VAL C 41 O PHE C 99 SHEET 5 AA1 6 LEU C 49 ILE C 55 -1 O GLU C 50 N ARG C 42 SHEET 6 AA1 6 THR C 62 TYR C 64 -1 O ASN C 63 N TRP C 54 SHEET 1 AA2 3 VAL C 22 LYS C 27 0 SHEET 2 AA2 3 THR C 82 LEU C 87 -1 O ALA C 83 N CYS C 26 SHEET 3 AA2 3 VAL C 72 ASP C 77 -1 N THR C 73 O GLU C 86 SHEET 1 AA3 3 THR B 251 ASP B 253 0 SHEET 2 AA3 3 PRO B 243 ILE B 245 -1 N CYS B 244 O TYR B 252 SHEET 3 AA3 3 ILE B 281 PRO B 282 -1 O ILE B 281 N ILE B 245 SHEET 1 AA4 5 SER D 24 ALA D 27 0 SHEET 2 AA4 5 THR D 121 VAL D 125 1 O ARG D 122 N VAL D 25 SHEET 3 AA4 5 ALA D 100 TRP D 107 -1 N ALA D 100 O LEU D 123 SHEET 4 AA4 5 THR D 50 GLN D 54 -1 N TYR D 52 O TYR D 103 SHEET 5 AA4 5 LYS D 61 ILE D 64 -1 O ILE D 64 N TRP D 51 SHEET 1 AA5 4 SER D 24 ALA D 27 0 SHEET 2 AA5 4 THR D 121 VAL D 125 1 O ARG D 122 N VAL D 25 SHEET 3 AA5 4 ALA D 100 TRP D 107 -1 N ALA D 100 O LEU D 123 SHEET 4 AA5 4 ARG D 115 PHE D 117 -1 O VAL D 116 N THR D 106 SHEET 1 AA6 3 VAL D 33 SER D 38 0 SHEET 2 AA6 3 SER D 86 ILE D 91 -1 O LEU D 89 N ILE D 35 SHEET 3 AA6 3 PHE D 78 SER D 79 -1 N SER D 79 O GLY D 90 SSBOND 1 CYS C 26 CYS C 100 1555 1555 2.02 SSBOND 2 CYS D 37 CYS D 104 1555 1555 2.04 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 302 1437 CONECT 1437 302 CONECT 3251 4223 CONECT 4223 3251 MASTER 158 0 0 6 24 0 0 6 2310 3 4 25 END