HEADER CYTOSOLIC PROTEIN 10-JUN-22 7Y3C TITLE CRYSTAL STRUCTURE OF TRIM7 BOUND TO RACO-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE TRIM7,E3 UBIQUITIN-PROTEIN COMPND 3 LIGASE TRIM7,TRIM7-RACO-1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: GLYCOGENIN-INTERACTING PROTEIN,RING FINGER PROTEIN 90, COMPND 6 TRIPARTITE MOTIF-CONTAINING PROTEIN 7; COMPND 7 EC: 2.3.2.27,2.3.2.27; COMPND 8 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: TRIM7, GNIP, RNF90; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E3 LIGASE, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.DONG,X.YAN REVDAT 2 29-NOV-23 7Y3C 1 REMARK REVDAT 1 03-AUG-22 7Y3C 0 JRNL AUTH Y.RU,X.YAN,B.ZHANG,L.SONG,Q.FENG,C.YE,Z.ZHOU,Z.YANG,Y.LI, JRNL AUTH 2 Z.ZHANG,Q.LI,W.MI,C.DONG JRNL TITL C-TERMINAL GLUTAMINE ACTS AS A C-DEGRON TARGETED BY E3 JRNL TITL 2 UBIQUITIN LIGASE TRIM7. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 18119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 35867826 JRNL DOI 10.1073/PNAS.2203218119 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 19577 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 920 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.9500 - 3.2700 1.00 2925 154 0.1410 0.1737 REMARK 3 2 3.2700 - 2.5900 1.00 2860 134 0.1627 0.2100 REMARK 3 3 2.5900 - 2.2700 1.00 2899 126 0.1771 0.1875 REMARK 3 4 2.2700 - 2.0600 1.00 2834 150 0.1632 0.1925 REMARK 3 5 2.0600 - 1.9200 0.92 2441 106 0.1797 0.2170 REMARK 3 6 1.9000 - 1.8000 0.81 2153 112 0.2056 0.2981 REMARK 3 7 1.8000 - 1.7100 0.90 2545 138 0.2400 0.2931 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.216 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.873 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1510 REMARK 3 ANGLE : 0.965 2064 REMARK 3 CHIRALITY : 0.060 227 REMARK 3 PLANARITY : 0.008 269 REMARK 3 DIHEDRAL : 6.576 218 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 31.4621 6.2106 -3.7482 REMARK 3 T TENSOR REMARK 3 T11: 0.1949 T22: 0.1518 REMARK 3 T33: 0.1755 T12: 0.0025 REMARK 3 T13: -0.0145 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 1.5139 L22: 1.3893 REMARK 3 L33: 1.6549 L12: -0.0980 REMARK 3 L13: -0.4878 L23: -0.0860 REMARK 3 S TENSOR REMARK 3 S11: 0.0129 S12: -0.0348 S13: -0.0165 REMARK 3 S21: -0.0115 S22: -0.0419 S23: 0.0766 REMARK 3 S31: -0.0658 S32: -0.0563 S33: 0.0267 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7Y3C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300026104. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19719 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 69.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 15.60 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.50600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6UMA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 26% W/V POLYETHYLENE GLYCOL 3,350, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.40533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.70267 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.55400 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 8.85133 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 44.25667 REMARK 290 REMARK 290 REMARK: NULL 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 LYS A 338 REMARK 465 GLU A 339 REMARK 465 GLU A 340 REMARK 465 LYS A 341 REMARK 465 VAL A 342 REMARK 465 GLY A 512 REMARK 465 GLY A 513 REMARK 465 SER A 514 REMARK 465 GLY A 515 REMARK 465 GLY A 516 REMARK 465 SER A 517 REMARK 465 GLY A 518 REMARK 465 GLY A 519 REMARK 465 SER A 520 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH1 ARG A 365 O HOH A 601 2.09 REMARK 500 O HOH A 724 O HOH A 726 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 634 O HOH A 648 5555 2.14 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 THR A 382 -52.14 -130.09 REMARK 500 REMARK 500 REMARK: NULL DBREF 7Y3C A 338 511 UNP Q9C029 TRIM7_HUMAN 338 511 DBREF 7Y3C A 521 531 PDB 7Y3C 7Y3C 521 531 SEQADV 7Y3C GLY A 512 UNP Q9C029 LINKER SEQADV 7Y3C GLY A 513 UNP Q9C029 LINKER SEQADV 7Y3C SER A 514 UNP Q9C029 LINKER SEQADV 7Y3C GLY A 515 UNP Q9C029 LINKER SEQADV 7Y3C GLY A 516 UNP Q9C029 LINKER SEQADV 7Y3C SER A 517 UNP Q9C029 LINKER SEQADV 7Y3C GLY A 518 UNP Q9C029 LINKER SEQADV 7Y3C GLY A 519 UNP Q9C029 LINKER SEQADV 7Y3C SER A 520 UNP Q9C029 LINKER SEQRES 1 A 194 LYS GLU GLU LYS VAL GLU LEU THR LEU ASP PRO ASP THR SEQRES 2 A 194 ALA ASN PRO ARG LEU ILE LEU SER LEU ASP LEU LYS GLY SEQRES 3 A 194 VAL ARG LEU GLY GLU ARG ALA GLN ASP LEU PRO ASN HIS SEQRES 4 A 194 PRO CYS ARG PHE ASP THR ASN THR ARG VAL LEU ALA SER SEQRES 5 A 194 CYS GLY PHE SER SER GLY ARG HIS HIS TRP GLU VAL GLU SEQRES 6 A 194 VAL GLY SER LYS ASP GLY TRP ALA PHE GLY VAL ALA ARG SEQRES 7 A 194 GLU SER VAL ARG ARG LYS GLY LEU THR PRO PHE THR PRO SEQRES 8 A 194 GLU GLU GLY VAL TRP ALA LEU GLN LEU ASN GLY GLY GLN SEQRES 9 A 194 TYR TRP ALA VAL THR SER PRO GLU ARG SER PRO LEU SER SEQRES 10 A 194 CYS GLY HIS LEU SER ARG VAL ARG VAL ALA LEU ASP LEU SEQRES 11 A 194 GLU VAL GLY ALA VAL SER PHE TYR ALA VAL GLU ASP MET SEQRES 12 A 194 ARG HIS LEU TYR THR PHE ARG VAL ASN PHE GLN GLU ARG SEQRES 13 A 194 VAL PHE PRO LEU PHE SER VAL CYS SER THR GLY THR TYR SEQRES 14 A 194 LEU ARG ILE TRP PRO GLY GLY SER GLY GLY SER GLY GLY SEQRES 15 A 194 SER SER VAL GLY ALA THR LEU SER MET LEU LEU GLN FORMUL 2 HOH *151(H2 O) HELIX 1 AA1 THR A 427 GLU A 430 5 4 HELIX 2 AA2 VAL A 522 LEU A 529 1 8 SHEET 1 AA1 7 LEU A 355 LEU A 357 0 SHEET 2 AA1 7 GLY A 363 LEU A 366 -1 O ARG A 365 N ILE A 356 SHEET 3 AA1 7 TYR A 506 TRP A 510 -1 O LEU A 507 N VAL A 364 SHEET 4 AA1 7 ARG A 396 VAL A 403 -1 N GLU A 402 O ARG A 508 SHEET 5 AA1 7 ARG A 460 ASP A 466 -1 O VAL A 463 N TRP A 399 SHEET 6 AA1 7 ALA A 471 ALA A 476 -1 O ALA A 471 N ASP A 466 SHEET 7 AA1 7 HIS A 482 ARG A 487 -1 O LEU A 483 N PHE A 474 SHEET 1 AA2 6 ARG A 385 LEU A 387 0 SHEET 2 AA2 6 VAL A 494 VAL A 500 -1 O PHE A 498 N VAL A 386 SHEET 3 AA2 6 TRP A 409 ARG A 415 -1 N ALA A 414 O PHE A 495 SHEET 4 AA2 6 VAL A 432 ASN A 438 -1 O TRP A 433 N VAL A 413 SHEET 5 AA2 6 GLN A 441 ALA A 444 -1 O TRP A 443 N GLN A 436 SHEET 6 AA2 6 SER A 451 LEU A 453 -1 O LEU A 453 N TYR A 442 CISPEP 1 SER A 447 PRO A 448 0 1.12 CRYST1 79.898 79.898 53.108 90.00 90.00 120.00 P 65 6 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 0.012516 0.007226 0.000000 0.00000 SCALE2 0.000000 0.014452 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018830 0.00000