HEADER LIGASE 02-NOV-06 2JMD TITLE SOLUTION STRUCTURE OF THE RING DOMAIN OF HUMAN TRAF6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TNF RECEPTOR-ASSOCIATED FACTOR 6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RING-TYPE DOMAIN, RESIDUES 66-124; COMPND 5 SYNONYM: INTERLEUKIN 1 SIGNAL TRANSDUCER, RING FINGER PROTEIN 85, COMPND 6 HTRAF6; COMPND 7 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: TRAF6, RNF85; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL23DE3 KEYWDS PROTEIN, ZINC-BINDING, HUMAN TNF RECEPTOR-ASSOCIATED FACTOR 6, ZN2+ KEYWDS 2 COORDINATION, LIGASE EXPDTA SOLUTION NMR NUMMDL 50 AUTHOR P.MERCIER,M.J.LEWIS,D.D.HAU,L.F.SALTIBUS,W.XIAO,L.SPYRACOPOULOS REVDAT 4 20-DEC-23 2JMD 1 REMARK REVDAT 3 09-MAR-22 2JMD 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2JMD 1 VERSN REVDAT 1 10-APR-07 2JMD 0 JRNL AUTH P.MERCIER,M.J.LEWIS,D.D.HAU,L.F.SALTIBUS,W.XIAO, JRNL AUTH 2 L.SPYRACOPOULOS JRNL TITL STRUCTURE, INTERACTIONS, AND DYNAMICS OF THE RING DOMAIN JRNL TITL 2 FROM HUMAN TRAF6 JRNL REF PROTEIN SCI. V. 16 602 2007 JRNL REFN ISSN 0961-8368 JRNL PMID 17327397 JRNL DOI 10.1110/PS.062358007 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.5, X-PLOR NIH 2.15 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CYANA'S INTERNAL PROTOCOL AND REMARK 3 REFINEMENT OF CYANA'S STRUCTURES IN EXPLICIT SOLVENT USING XPLOR- REMARK 3 NIH REMARK 4 REMARK 4 2JMD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000100013. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99% 13C, U-99% 15N] REMARK 210 HTRAF6, 50 MM PHOSPHATE, 150 MM REMARK 210 NACL, PH 7.5, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HNHA; 3D HNHB; 3D HCCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 2D 1H-13C HSQC; 2D 1H-15N HSQC; REMARK 210 3D HACA(CO)CANHH; 3D H(CC)-TOCSY- REMARK 210 (CO)NNH; 3D (H)CCTOCSY(CO)NNH; REMARK 210 2D (HB)CB(CGCD)HD; 2D (HB) REMARK 210 CB(CGCDCE)HE; 3D HNN(CO,CA) REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, NMRVIEW 6.5, REMARK 210 PROCHECKNMR 3.5.4, X-PLOR NIH REMARK 210 2.15, VNMRJ 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 50 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 TYR A 7 76.68 48.70 REMARK 500 1 GLU A 18 -16.23 69.23 REMARK 500 1 ALA A 19 91.50 47.72 REMARK 500 1 ALA A 40 -66.68 -91.95 REMARK 500 2 MET A 14 -71.65 -99.14 REMARK 500 2 ALA A 15 -169.87 -173.13 REMARK 500 2 ALA A 19 76.07 52.84 REMARK 500 2 ASP A 39 -53.74 -122.16 REMARK 500 2 VAL A 46 -74.67 -86.35 REMARK 500 3 MET A 14 -71.00 -96.08 REMARK 500 3 ALA A 15 -158.28 178.77 REMARK 500 3 ALA A 19 81.36 53.76 REMARK 500 4 LEU A 3 -48.92 71.55 REMARK 500 4 MET A 14 -65.88 -95.64 REMARK 500 4 ALA A 19 81.71 61.14 REMARK 500 4 ALA A 40 -79.08 -92.80 REMARK 500 5 MET A 14 -68.36 -95.81 REMARK 500 5 ALA A 15 -159.11 -177.47 REMARK 500 5 ARG A 17 -73.29 -76.35 REMARK 500 5 ALA A 19 84.30 60.42 REMARK 500 5 PHE A 57 121.18 68.35 REMARK 500 6 MET A 14 -73.78 -102.50 REMARK 500 6 ALA A 15 -173.24 -170.34 REMARK 500 6 ALA A 19 81.79 57.75 REMARK 500 6 ALA A 40 -66.90 -92.59 REMARK 500 6 PHE A 57 135.43 66.01 REMARK 500 6 ASN A 60 -22.29 75.33 REMARK 500 6 ALA A 62 78.46 -111.88 REMARK 500 7 SER A 5 37.34 -95.74 REMARK 500 8 ALA A 19 87.50 58.26 REMARK 500 8 ALA A 40 -75.07 -84.05 REMARK 500 8 VAL A 46 -74.31 -71.74 REMARK 500 9 ALA A 19 81.70 58.81 REMARK 500 9 ASP A 39 -56.82 -136.57 REMARK 500 9 HIS A 42 34.09 -84.63 REMARK 500 9 VAL A 46 -74.10 -65.79 REMARK 500 9 ASP A 59 104.46 -47.54 REMARK 500 10 TYR A 7 38.22 -83.69 REMARK 500 10 MET A 14 -67.41 -93.54 REMARK 500 10 ALA A 15 -167.72 -176.96 REMARK 500 10 ALA A 19 83.16 51.43 REMARK 500 10 ALA A 40 -68.36 -92.90 REMARK 500 11 MET A 14 -68.33 -96.16 REMARK 500 11 ALA A 15 -161.35 178.33 REMARK 500 11 ALA A 19 74.50 56.22 REMARK 500 11 ASP A 39 -56.52 -122.08 REMARK 500 11 ALA A 40 -71.09 -85.76 REMARK 500 11 HIS A 42 30.12 -83.30 REMARK 500 12 CYS A 9 107.88 -59.19 REMARK 500 12 MET A 14 -67.23 -98.30 REMARK 500 REMARK 500 THIS ENTRY HAS 233 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 65 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 9 SG REMARK 620 2 CYS A 12 SG 102.4 REMARK 620 3 CYS A 29 SG 103.1 121.5 REMARK 620 4 CYS A 32 SG 112.4 107.7 109.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 66 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 HIS A 26 ND1 80.3 REMARK 620 3 CYS A 44 SG 122.5 129.8 REMARK 620 4 ASP A 47 OD1 140.8 84.3 95.0 REMARK 620 5 ASP A 47 OD2 89.6 116.5 108.3 65.6 REMARK 620 N 1 2 3 4 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 65 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 66 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LB4 RELATED DB: PDB REMARK 900 TNF RECEPTOR-ASSOCIATED FACTOR 6 REMARK 900 RELATED ID: 1JM7 RELATED DB: PDB REMARK 900 BRCA1/BARD1 RING HETERODIMER REMARK 900 RELATED ID: 1E4U RELATED DB: PDB REMARK 900 N-TERMINAL RING DOMAIN FROM HUMAN NOT4 REMARK 900 RELATED ID: 1CHC RELATED DB: PDB REMARK 900 RING DOMAIN FROM EQUINE HERPES VIRUS-1 REMARK 900 RELATED ID: 15014 RELATED DB: BMRB DBREF 2JMD A 6 63 UNP Q9Y4K3 TRAF6_HUMAN 67 124 SEQADV 2JMD GLY A 1 UNP Q9Y4K3 CLONING ARTIFACT SEQADV 2JMD PRO A 2 UNP Q9Y4K3 CLONING ARTIFACT SEQADV 2JMD LEU A 3 UNP Q9Y4K3 CLONING ARTIFACT SEQADV 2JMD GLY A 4 UNP Q9Y4K3 CLONING ARTIFACT SEQADV 2JMD SER A 5 UNP Q9Y4K3 CLONING ARTIFACT SEQRES 1 A 63 GLY PRO LEU GLY SER LYS TYR GLU CYS PRO ILE CYS LEU SEQRES 2 A 63 MET ALA LEU ARG GLU ALA VAL GLN THR PRO CYS GLY HIS SEQRES 3 A 63 ARG PHE CYS LYS ALA CYS ILE ILE LYS SER ILE ARG ASP SEQRES 4 A 63 ALA GLY HIS LYS CYS PRO VAL ASP ASN GLU ILE LEU LEU SEQRES 5 A 63 GLU ASN GLN LEU PHE PRO ASP ASN PHE ALA LYS HET ZN A 65 1 HET ZN A 66 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 ILE A 33 ARG A 38 1 6 HELIX 2 2 LEU A 52 LEU A 56 5 5 SHEET 1 A 2 GLU A 8 CYS A 9 0 SHEET 2 A 2 MET A 14 ALA A 15 -1 O MET A 14 N CYS A 9 SHEET 1 B 3 ARG A 27 PHE A 28 0 SHEET 2 B 3 VAL A 20 GLN A 21 -1 N VAL A 20 O PHE A 28 SHEET 3 B 3 PHE A 57 PRO A 58 -1 O PHE A 57 N GLN A 21 LINK SG CYS A 9 ZN ZN A 65 1555 1555 2.46 LINK SG CYS A 12 ZN ZN A 65 1555 1555 2.16 LINK SG CYS A 24 ZN ZN A 66 1555 1555 2.18 LINK ND1 HIS A 26 ZN ZN A 66 1555 1555 2.69 LINK SG CYS A 29 ZN ZN A 65 1555 1555 2.28 LINK SG CYS A 32 ZN ZN A 65 1555 1555 2.27 LINK SG CYS A 44 ZN ZN A 66 1555 1555 2.26 LINK OD1 ASP A 47 ZN ZN A 66 1555 1555 1.91 LINK OD2 ASP A 47 ZN ZN A 66 1555 1555 2.04 SITE 1 AC1 4 CYS A 9 CYS A 12 CYS A 29 CYS A 32 SITE 1 AC2 4 CYS A 24 HIS A 26 CYS A 44 ASP A 47 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