HEADER SIGNALING PROTEIN 23-NOV-18 6I9H TITLE SOLUTION STRUCTURE OF TRIM28 RING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION INTERMEDIARY FACTOR 1-BETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TIF1-BETA,E3 SUMO-PROTEIN LIGASE TRIM28,KRAB-ASSOCIATED COMPND 5 PROTEIN 1,KAP-1,KRAB-INTERACTING PROTEIN 1,KRIP-1,NUCLEAR COREPRESSOR COMPND 6 KAP-1,RING FINGER PROTEIN 96,RING-TYPE E3 UBIQUITIN TRANSFERASE TIF1- COMPND 7 BETA,TRIPARTITE MOTIF-CONTAINING PROTEIN 28; COMPND 8 EC: 2.3.2.27; COMPND 9 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: TRIM28, KAP1, RNF96, TIF1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRIM, E3 LIGASE, ENZYME, UBIQUITIN, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 18 AUTHOR R.V.STEVENS,D.ESPOSITO,K.RITTINGER REVDAT 3 14-JUN-23 6I9H 1 REMARK REVDAT 2 08-MAY-19 6I9H 1 JRNL REMARK REVDAT 1 01-MAY-19 6I9H 0 JRNL AUTH R.V.STEVENS,D.ESPOSITO,K.RITTINGER JRNL TITL CHARACTERISATION OF CLASS VI TRIM RING DOMAINS: LINKING RING JRNL TITL 2 ACTIVITY TO C-TERMINAL DOMAIN IDENTITY. JRNL REF LIFE SCI ALLIANCE V. 2 2019 JRNL REFN ESSN 2575-1077 JRNL PMID 31028095 JRNL DOI 10.26508/LSA.201900295 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6I9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1200013055. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 100; 100 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-15N] TRIM28 RING, 90% REMARK 210 H2O/10% D2O; 1 MM [U-13C; U-15N] REMARK 210 TRIM28 RING, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HN(CO)CA; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HNCO; REMARK 210 3D HN(CA)CO; 3D HCCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D 1H-13C NOESY AROMATIC; 2D 1H- REMARK 210 15N HSQC; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS, ARIA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-18 REMARK 465 RES C SSSEQI REMARK 465 GLY A 52 REMARK 465 PRO A 53 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 1 GLU A 57 37.42 -89.39 REMARK 500 1 LEU A 62 -88.04 -162.56 REMARK 500 1 GLU A 63 -78.92 167.33 REMARK 500 1 GLU A 77 70.06 46.71 REMARK 500 1 LEU A 84 46.37 75.52 REMARK 500 1 ASP A 111 82.93 68.68 REMARK 500 1 THR A 113 -119.33 -116.16 REMARK 500 1 VAL A 119 -60.86 -94.35 REMARK 500 1 VAL A 130 103.49 -38.76 REMARK 500 1 GLU A 131 -21.31 161.97 REMARK 500 1 MET A 135 -168.53 171.03 REMARK 500 2 LEU A 62 -85.53 -169.39 REMARK 500 2 GLU A 63 -80.09 167.10 REMARK 500 2 GLU A 77 71.76 54.30 REMARK 500 2 LEU A 84 51.51 74.02 REMARK 500 2 ALA A 108 -56.75 176.20 REMARK 500 2 ASP A 111 87.23 77.38 REMARK 500 2 THR A 113 -122.84 -116.81 REMARK 500 2 ASP A 116 92.01 -67.37 REMARK 500 2 GLN A 122 100.76 -170.31 REMARK 500 2 VAL A 130 104.74 -39.32 REMARK 500 2 GLU A 131 -25.02 162.86 REMARK 500 2 ASN A 132 57.55 -104.60 REMARK 500 2 PHE A 134 -74.97 -102.18 REMARK 500 2 SER A 138 -26.79 176.72 REMARK 500 3 LEU A 62 -89.22 -163.34 REMARK 500 3 GLU A 63 -79.99 165.41 REMARK 500 3 GLU A 77 70.02 56.56 REMARK 500 3 LEU A 84 41.68 73.90 REMARK 500 3 ASP A 111 74.46 70.87 REMARK 500 3 THR A 113 -119.31 -115.44 REMARK 500 3 VAL A 119 -63.09 -95.64 REMARK 500 3 SER A 126 53.56 -108.04 REMARK 500 3 ILE A 129 -171.10 -62.87 REMARK 500 3 VAL A 130 109.43 -37.90 REMARK 500 3 GLU A 131 -30.78 167.96 REMARK 500 3 SER A 138 -75.88 -177.56 REMARK 500 4 LEU A 62 -86.60 -168.28 REMARK 500 4 GLU A 63 -78.38 166.94 REMARK 500 4 LEU A 84 47.94 75.41 REMARK 500 4 ALA A 109 29.64 47.10 REMARK 500 4 ASP A 111 82.38 73.43 REMARK 500 4 THR A 113 -119.99 -117.67 REMARK 500 4 VAL A 119 -62.54 -92.49 REMARK 500 4 ILE A 129 -169.83 -64.06 REMARK 500 4 VAL A 130 104.32 -39.05 REMARK 500 4 GLU A 131 -13.24 162.91 REMARK 500 4 TYR A 133 105.77 -42.09 REMARK 500 4 PHE A 134 -74.40 -85.05 REMARK 500 4 SER A 138 96.63 -179.54 REMARK 500 REMARK 500 THIS ENTRY HAS 236 RAMACHANDRAN OUTLIERS. 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 A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 65 SG REMARK 620 2 CYS A 68 SG 106.5 REMARK 620 3 CYS A 88 SG 96.7 96.0 REMARK 620 4 CYS A 91 SG 121.0 127.1 99.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 83 SG REMARK 620 2 HIS A 85 ND1 83.5 REMARK 620 3 CYS A 117 SG 99.2 99.9 REMARK 620 4 CYS A 120 SG 102.2 133.6 123.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34330 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF TRIM28 RING DOMAIN DBREF 6I9H A 54 145 UNP Q13263 TIF1B_HUMAN 54 145 SEQADV 6I9H GLY A 52 UNP Q13263 EXPRESSION TAG SEQADV 6I9H PRO A 53 UNP Q13263 EXPRESSION TAG SEQRES 1 A 94 GLY PRO GLY GLY ALA GLU ALA LEU GLU LEU LEU GLU HIS SEQRES 2 A 94 CYS GLY VAL CYS ARG GLU ARG LEU ARG PRO GLU ARG GLU SEQRES 3 A 94 PRO ARG LEU LEU PRO CYS LEU HIS SER ALA CYS SER ALA SEQRES 4 A 94 CYS LEU GLY PRO ALA ALA PRO ALA ALA ALA ASN SER SER SEQRES 5 A 94 GLY ASP GLY GLY ALA ALA GLY ASP GLY THR VAL VAL ASP SEQRES 6 A 94 CYS PRO VAL CYS LYS GLN GLN CYS PHE SER LYS ASP ILE SEQRES 7 A 94 VAL GLU ASN TYR PHE MET ARG ASP SER GLY SER LYS ALA SEQRES 8 A 94 ALA THR ASP HET ZN A 201 1 HET ZN A 202 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 ALA A 58 LEU A 61 5 4 HELIX 2 AA2 ARG A 73 ARG A 76 5 4 HELIX 3 AA3 SER A 89 ALA A 96 1 8 SHEET 1 AA1 2 GLY A 55 ALA A 56 0 SHEET 2 AA1 2 SER A 138 GLY A 139 -1 O GLY A 139 N GLY A 55 SHEET 1 AA2 2 PRO A 78 LEU A 80 0 SHEET 2 AA2 2 SER A 86 CYS A 88 -1 O ALA A 87 N ARG A 79 LINK SG CYS A 65 ZN ZN A 202 1555 1555 2.39 LINK SG CYS A 68 ZN ZN A 202 1555 1555 2.38 LINK SG CYS A 83 ZN ZN A 201 1555 1555 2.39 LINK ND1 HIS A 85 ZN ZN A 201 1555 1555 2.12 LINK SG CYS A 88 ZN ZN A 202 1555 1555 2.40 LINK SG CYS A 91 ZN ZN A 202 1555 1555 2.38 LINK SG CYS A 117 ZN ZN A 201 1555 1555 2.38 LINK SG CYS A 120 ZN ZN A 201 1555 1555 2.38 SITE 1 AC1 5 CYS A 83 HIS A 85 CYS A 117 VAL A 119 SITE 2 AC1 5 CYS A 120 SITE 1 AC2 4 CYS A 65 CYS A 68 CYS A 88 CYS A 91 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 MODEL 1