HEADER ANTIVIRAL PROTEIN 08-MAR-22 7X6Y TITLE TRIM7 IN COMPLEX WITH C-TERMINAL PEPTIDE OF NSP5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE TRIM7; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLYCOGENIN-INTERACTING PROTEIN,RING FINGER PROTEIN 90, COMPND 5 TRIPARTITE MOTIF-CONTAINING PROTEIN 7; COMPND 6 EC: 2.3.2.27; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 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; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 11 2; SOURCE 12 ORGANISM_TAXID: 2697049 KEYWDS ANTIVIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,X.LIANG,X.Z.LI REVDAT 4 29-NOV-23 7X6Y 1 REMARK REVDAT 3 09-NOV-22 7X6Y 1 JRNL REVDAT 2 26-OCT-22 7X6Y 1 JRNL REVDAT 1 10-AUG-22 7X6Y 0 JRNL AUTH X.LIANG,J.XIAO,X.LI,Y.LIU,Y.LU,Y.WEN,Z.LI,X.CHE,Y.MA, JRNL AUTH 2 X.ZHANG,Y.ZHANG,D.JIAN,P.WANG,C.XUAN,G.YU,L.LI,H.ZHANG JRNL TITL A C-TERMINAL GLUTAMINE RECOGNITION MECHANISM REVEALED BY E3 JRNL TITL 2 LIGASE TRIM7 STRUCTURES. JRNL REF NAT.CHEM.BIOL. V. 18 1214 2022 JRNL REFN ESSN 1552-4469 JRNL PMID 35982226 JRNL DOI 10.1038/S41589-022-01128-X REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 39125 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1976 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 26.1600 - 3.3400 1.00 2739 135 0.1509 0.1506 REMARK 3 2 3.3400 - 2.6500 1.00 2647 158 0.1486 0.1607 REMARK 3 3 2.6500 - 2.3200 1.00 2684 132 0.1486 0.1676 REMARK 3 4 2.3200 - 2.1100 1.00 2637 149 0.1396 0.1753 REMARK 3 5 2.1100 - 1.9600 1.00 2627 165 0.1202 0.1517 REMARK 3 6 1.9500 - 1.8400 1.00 2664 145 0.1275 0.1526 REMARK 3 7 1.8400 - 1.7500 1.00 2639 139 0.1204 0.1594 REMARK 3 8 1.7500 - 1.6700 1.00 2674 125 0.1298 0.1503 REMARK 3 9 1.6700 - 1.6100 1.00 2637 144 0.1322 0.2170 REMARK 3 10 1.6100 - 1.5500 1.00 2643 150 0.1424 0.1883 REMARK 3 11 1.5500 - 1.5000 1.00 2644 104 0.1386 0.1738 REMARK 3 12 1.5000 - 1.4600 1.00 2631 161 0.1509 0.1810 REMARK 3 13 1.4600 - 1.4200 1.00 2664 139 0.1630 0.2159 REMARK 3 14 1.4200 - 1.3900 1.00 2619 130 0.1924 0.2389 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.109 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.359 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.17 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 : 0.005 1433 REMARK 3 ANGLE : 0.871 1948 REMARK 3 CHIRALITY : 0.082 210 REMARK 3 PLANARITY : 0.008 254 REMARK 3 DIHEDRAL : 6.817 195 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7X6Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028216. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39139 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 26.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: 7W0Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, TRIS, LIQUID DIFFUSION, TEMPERATURE 291.15K 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 35.38867 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 17.69433 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 26.54150 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 8.84717 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 44.23583 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 REMARK 465 LYS A 4 REMARK 465 VAL A 5 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 O HOH A 202 O HOH A 389 1.94 REMARK 500 O THR A 166 O HOH A 201 1.98 REMARK 500 O HOH A 207 O HOH A 220 2.04 REMARK 500 O HOH A 333 O HOH A 407 2.12 REMARK 500 O HOH A 354 O HOH A 355 2.13 REMARK 500 O HOH A 205 O HOH A 354 2.18 REMARK 500 NE ARG A 28 O HOH A 202 2.19 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 377 O HOH A 389 5555 2.17 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 45 -53.72 -133.83 REMARK 500 SER A 117 52.62 -98.45 REMARK 500 REMARK 500 REMARK: NULL DBREF 7X6Y A 1 174 UNP Q9C029 TRIM7_HUMAN 338 511 DBREF 7X6Y B -1 5 PDB 7X6Y 7X6Y -1 5 SEQRES 1 A 174 LYS GLU GLU LYS VAL GLU LEU THR LEU ASP PRO ASP THR SEQRES 2 A 174 ALA ASN PRO ARG LEU ILE LEU SER LEU ASP LEU LYS GLY SEQRES 3 A 174 VAL ARG LEU GLY GLU ARG ALA GLN ASP LEU PRO ASN HIS SEQRES 4 A 174 PRO CYS ARG PHE ASP THR ASN THR ARG VAL LEU ALA SER SEQRES 5 A 174 CYS GLY PHE SER SER GLY ARG HIS HIS TRP GLU VAL GLU SEQRES 6 A 174 VAL GLY SER LYS ASP GLY TRP ALA PHE GLY VAL ALA ARG SEQRES 7 A 174 GLU SER VAL ARG ARG LYS GLY LEU THR PRO PHE THR PRO SEQRES 8 A 174 GLU GLU GLY VAL TRP ALA LEU GLN LEU ASN GLY GLY GLN SEQRES 9 A 174 TYR TRP ALA VAL THR SER PRO GLU ARG SER PRO LEU SER SEQRES 10 A 174 CYS GLY HIS LEU SER ARG VAL ARG VAL ALA LEU ASP LEU SEQRES 11 A 174 GLU VAL GLY ALA VAL SER PHE TYR ALA VAL GLU ASP MET SEQRES 12 A 174 ARG HIS LEU TYR THR PHE ARG VAL ASN PHE GLN GLU ARG SEQRES 13 A 174 VAL PHE PRO LEU PHE SER VAL CYS SER THR GLY THR TYR SEQRES 14 A 174 LEU ARG ILE TRP PRO SEQRES 1 B 7 CYS SER GLY VAL THR PHE GLN FORMUL 3 HOH *221(H2 O) HELIX 1 AA1 THR A 90 GLU A 93 5 4 HELIX 2 AA2 GLY B 1 GLN B 5 5 5 SHEET 1 AA1 7 LEU A 18 LEU A 20 0 SHEET 2 AA1 7 GLY A 26 LEU A 29 -1 O ARG A 28 N ILE A 19 SHEET 3 AA1 7 LEU A 170 TRP A 173 -1 O LEU A 170 N VAL A 27 SHEET 4 AA1 7 ARG A 59 VAL A 66 -1 N GLU A 65 O ARG A 171 SHEET 5 AA1 7 ARG A 123 ASP A 129 -1 O VAL A 126 N TRP A 62 SHEET 6 AA1 7 ALA A 134 ALA A 139 -1 O ALA A 134 N ASP A 129 SHEET 7 AA1 7 HIS A 145 ARG A 150 -1 O LEU A 146 N PHE A 137 SHEET 1 AA2 6 ARG A 48 LEU A 50 0 SHEET 2 AA2 6 VAL A 157 VAL A 163 -1 O PHE A 161 N VAL A 49 SHEET 3 AA2 6 TRP A 72 ARG A 78 -1 N ALA A 77 O PHE A 158 SHEET 4 AA2 6 VAL A 95 ASN A 101 -1 O TRP A 96 N VAL A 76 SHEET 5 AA2 6 GLN A 104 ALA A 107 -1 O TRP A 106 N GLN A 99 SHEET 6 AA2 6 SER A 114B LEU A 116 -1 O LEU A 116 N TYR A 105 CISPEP 1 SER A 110 PRO A 113 0 1.40 CRYST1 79.915 79.915 53.083 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 0.012513 0.007225 0.000000 0.00000 SCALE2 0.000000 0.014449 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018838 0.00000