HEADER LIGASE 07-JUL-11 3ZTG TITLE SOLUTION STRUCTURE OF THE RING FINGER-LIKE DOMAIN OF RETINOBLASTOMA TITLE 2 BINDING PROTEIN-6 (RBBP6) COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RBBP6; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RING FINGER-LIKE DOMAIN, RESIDUES 249-335; COMPND 5 SYNONYM: RETINOBLASTOMA BINDING PROTEIN-6, PROLIFERATION POTENTIAL- COMPND 6 RELATED PROTEIN, PROTEIN P2P-R, RETINOBLASTOMA-BINDING Q PROTEIN 1, COMPND 7 RBQ-1, RETINOBLASTOMA-BINDING PROTEIN 6, P53-ASSOCIATED CELLULAR COMPND 8 PROTEIN OF TESTIS; COMPND 9 EC: 6.3.2.-; COMPND 10 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-6P-2 KEYWDS LIGASE, RBBP6, PACT, U-BOX, MRNA PROCESSING, MRNA SPLICING EXPDTA SOLUTION NMR NUMMDL 32 AUTHOR M.A.KAPPO,E.AB,R.A.ATKINSON,A.FARO,V.MULEYA,T.MULAUDZI,J.O.POOLE, AUTHOR 2 J.M.MCKENZIE,D.J.R.PUGH REVDAT 4 19-JUN-24 3ZTG 1 REMARK REVDAT 3 14-JUN-23 3ZTG 1 REMARK LINK ATOM REVDAT 2 14-MAR-12 3ZTG 1 JRNL REVDAT 1 07-DEC-11 3ZTG 0 JRNL AUTH M.A.KAPPO,E.AB,F.HASSEM,R.A.ATKINSON,A.FARO,V.MULEYA, JRNL AUTH 2 T.MULAUDZI,J.O.POOLE,J.M.MCKENZIE,M.CHIBI,J.C.MOOLMAN-SMOOK, JRNL AUTH 3 D.J.G.REES,D.J.R.PUGH JRNL TITL SOLUTION STRUCTURE OF THE RING FINGER-LIKE DOMAIN OF JRNL TITL 2 RETINOBLASTOMA BINDING PROTEIN-6 (RBBP6) SUGGESTS IT JRNL TITL 3 FUNCTIONS AS A U-BOX JRNL REF J.BIOL.CHEM. V. 287 7146 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22130672 JRNL DOI 10.1074/JBC.M110.217059 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 2.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3ZTG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1290048934. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N-HSQC-NOESY 13C-HSQC- NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, NMRVIEW REMARK 210 METHOD USED : CYANA FOLLOWED BY HADDOCK REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 32 REMARK 210 CONFORMERS, SELECTION CRITERIA : HADDOCK ENERGY, RAMACHANDRAN REMARK 210 QUALITY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DTERMINED USING THE FOLLOWING NMR REMARK 210 EXPERIMENTS 2D-NOESY 13C-NOESY 15N-NOESY 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 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 OD1 ASP B 251 HG1 THR B 326 1.57 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 LEU A 257 12.92 -160.75 REMARK 500 1 CYS A 275 -48.35 -134.59 REMARK 500 1 PRO A 297 34.69 -81.38 REMARK 500 1 THR A 298 -47.27 -158.08 REMARK 500 1 ASP A 303 44.19 -155.42 REMARK 500 1 VAL A 304 -163.59 -106.62 REMARK 500 1 SER A 305 145.67 -177.40 REMARK 500 1 LYS A 334 55.32 -100.49 REMARK 500 1 ASP B 251 135.03 175.89 REMARK 500 1 LEU B 257 19.82 -161.46 REMARK 500 1 CYS B 275 -51.43 -138.80 REMARK 500 1 PRO B 297 31.65 -81.26 REMARK 500 1 THR B 298 -47.68 -155.53 REMARK 500 1 ASP B 303 44.53 -158.01 REMARK 500 1 VAL B 304 -164.92 -108.02 REMARK 500 1 SER B 305 146.04 -176.81 REMARK 500 1 LYS B 334 50.95 -96.10 REMARK 500 2 ASP A 251 141.70 179.91 REMARK 500 2 LEU A 257 15.31 -162.55 REMARK 500 2 CYS A 275 -46.45 -136.93 REMARK 500 2 PRO A 297 38.90 -81.92 REMARK 500 2 THR A 298 -50.07 -164.45 REMARK 500 2 ASN A 302 35.40 -146.40 REMARK 500 2 ASP A 303 36.56 -156.74 REMARK 500 2 VAL A 304 -159.18 -101.48 REMARK 500 2 SER A 305 147.06 177.96 REMARK 500 2 THR A 329 -179.85 -178.03 REMARK 500 2 LYS A 334 44.02 -91.48 REMARK 500 2 LEU B 257 24.59 -158.14 REMARK 500 2 CYS B 275 -47.96 -138.95 REMARK 500 2 PRO B 297 23.13 -75.96 REMARK 500 2 THR B 298 -46.95 -156.44 REMARK 500 2 ASP B 303 32.58 -147.68 REMARK 500 3 LEU A 257 12.00 -163.81 REMARK 500 3 CYS A 275 -49.88 -141.84 REMARK 500 3 PRO A 297 33.49 -81.35 REMARK 500 3 THR A 298 -48.03 -159.17 REMARK 500 3 ASN A 302 21.42 -142.84 REMARK 500 3 ASP A 303 54.66 -150.36 REMARK 500 3 THR A 329 164.88 177.82 REMARK 500 3 LEU B 257 18.38 -160.15 REMARK 500 3 CYS B 275 -46.39 -136.49 REMARK 500 3 PRO B 297 38.99 -81.53 REMARK 500 3 THR B 298 -48.31 -164.62 REMARK 500 3 ASP B 303 57.94 -157.94 REMARK 500 4 ASP A 255 1.46 -69.51 REMARK 500 4 LEU A 257 13.41 -162.78 REMARK 500 4 CYS A 275 -52.04 -135.74 REMARK 500 4 PRO A 297 30.03 -80.37 REMARK 500 4 THR A 298 -49.39 -154.97 REMARK 500 REMARK 500 THIS ENTRY HAS 442 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 A1336 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 259 SG REMARK 620 2 CYS A 262 SG 107.1 REMARK 620 3 CYS A 280 SG 109.5 114.4 REMARK 620 4 CYS A 283 SG 120.9 104.2 100.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1337 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 274 SG REMARK 620 2 CYS A 275 SG 104.7 REMARK 620 3 CYS A 296 SG 108.8 114.0 REMARK 620 4 CYS A 299 SG 116.4 108.6 104.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1336 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 259 SG REMARK 620 2 CYS B 262 SG 98.3 REMARK 620 3 CYS B 280 SG 100.7 114.2 REMARK 620 4 CYS B 283 SG 121.4 112.7 108.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1337 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 274 SG REMARK 620 2 CYS B 275 SG 103.2 REMARK 620 3 CYS B 296 SG 109.7 118.2 REMARK 620 4 CYS B 299 SG 115.0 106.2 105.0 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 1336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1337 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Y8X RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE RING FINGER-LIKE DOMAIN OF RETINOBLASTOMA REMARK 900 BINDING PROTEIN-6 (RBBP6) REMARK 900 RELATED ID: 2C7H RELATED DB: PDB REMARK 900 SOLUTION NMR STRUCTURE OF THE DWNN DOMAIN FROM HUMAN RBBP6 REMARK 900 RELATED ID: 17772 RELATED DB: BMRB DBREF 3ZTG A 249 335 UNP Q7Z6E9 RBBP6_HUMAN 249 335 DBREF 3ZTG B 249 335 UNP Q7Z6E9 RBBP6_HUMAN 249 335 SEQADV 3ZTG GLY A 244 UNP Q7Z6E9 EXPRESSION TAG SEQADV 3ZTG PRO A 245 UNP Q7Z6E9 EXPRESSION TAG SEQADV 3ZTG LEU A 246 UNP Q7Z6E9 EXPRESSION TAG SEQADV 3ZTG GLY A 247 UNP Q7Z6E9 EXPRESSION TAG SEQADV 3ZTG SER A 248 UNP Q7Z6E9 EXPRESSION TAG SEQADV 3ZTG GLY B 244 UNP Q7Z6E9 EXPRESSION TAG SEQADV 3ZTG PRO B 245 UNP Q7Z6E9 EXPRESSION TAG SEQADV 3ZTG LEU B 246 UNP Q7Z6E9 EXPRESSION TAG SEQADV 3ZTG GLY B 247 UNP Q7Z6E9 EXPRESSION TAG SEQADV 3ZTG SER B 248 UNP Q7Z6E9 EXPRESSION TAG SEQRES 1 A 92 GLY PRO LEU GLY SER GLU ASP ASP PRO ILE PRO ASP GLU SEQRES 2 A 92 LEU LEU CYS LEU ILE CYS LYS ASP ILE MET THR ASP ALA SEQRES 3 A 92 VAL VAL ILE PRO CYS CYS GLY ASN SER TYR CYS ASP GLU SEQRES 4 A 92 CYS ILE ARG THR ALA LEU LEU GLU SER ASP GLU HIS THR SEQRES 5 A 92 CYS PRO THR CYS HIS GLN ASN ASP VAL SER PRO ASP ALA SEQRES 6 A 92 LEU ILE ALA ASN LYS PHE LEU ARG GLN ALA VAL ASN ASN SEQRES 7 A 92 PHE LYS ASN GLU THR GLY TYR THR LYS ARG LEU ARG LYS SEQRES 8 A 92 GLN SEQRES 1 B 92 GLY PRO LEU GLY SER GLU ASP ASP PRO ILE PRO ASP GLU SEQRES 2 B 92 LEU LEU CYS LEU ILE CYS LYS ASP ILE MET THR ASP ALA SEQRES 3 B 92 VAL VAL ILE PRO CYS CYS GLY ASN SER TYR CYS ASP GLU SEQRES 4 B 92 CYS ILE ARG THR ALA LEU LEU GLU SER ASP GLU HIS THR SEQRES 5 B 92 CYS PRO THR CYS HIS GLN ASN ASP VAL SER PRO ASP ALA SEQRES 6 B 92 LEU ILE ALA ASN LYS PHE LEU ARG GLN ALA VAL ASN ASN SEQRES 7 B 92 PHE LYS ASN GLU THR GLY TYR THR LYS ARG LEU ARG LYS SEQRES 8 B 92 GLN HET ZN A1336 1 HET ZN A1337 1 HET ZN B1336 1 HET ZN B1337 1 HETNAM ZN ZINC ION FORMUL 3 ZN 4(ZN 2+) HELIX 1 1 CYS A 280 SER A 291 1 12 HELIX 2 2 ASN A 312 THR A 326 1 15 HELIX 3 3 CYS B 280 SER B 291 1 12 HELIX 4 4 ASN B 312 GLY B 327 1 16 SHEET 1 AA 2 LEU A 258 CYS A 259 0 SHEET 2 AA 2 ASP A 264 ILE A 265 -1 O ASP A 264 N CYS A 259 SHEET 1 AB 3 SER A 278 TYR A 279 0 SHEET 2 AB 3 VAL A 270 VAL A 271 -1 O VAL A 270 N TYR A 279 SHEET 3 AB 3 ILE A 310 ALA A 311 -1 O ILE A 310 N VAL A 271 SHEET 1 BA 2 LEU B 258 CYS B 259 0 SHEET 2 BA 2 ASP B 264 ILE B 265 -1 O ASP B 264 N CYS B 259 SHEET 1 BB 3 SER B 278 TYR B 279 0 SHEET 2 BB 3 VAL B 270 VAL B 271 -1 O VAL B 270 N TYR B 279 SHEET 3 BB 3 ILE B 310 ALA B 311 -1 O ILE B 310 N VAL B 271 LINK SG CYS A 259 ZN ZN A1336 1555 1555 2.23 LINK SG CYS A 262 ZN ZN A1336 1555 1555 2.07 LINK SG CYS A 274 ZN ZN A1337 1555 1555 2.05 LINK SG CYS A 275 ZN ZN A1337 1555 1555 2.46 LINK SG CYS A 280 ZN ZN A1336 1555 1555 2.07 LINK SG CYS A 283 ZN ZN A1336 1555 1555 2.40 LINK SG CYS A 296 ZN ZN A1337 1555 1555 2.16 LINK SG CYS A 299 ZN ZN A1337 1555 1555 2.18 LINK SG CYS B 259 ZN ZN B1336 1555 1555 2.48 LINK SG CYS B 262 ZN ZN B1336 1555 1555 2.10 LINK SG CYS B 274 ZN ZN B1337 1555 1555 2.06 LINK SG CYS B 275 ZN ZN B1337 1555 1555 2.48 LINK SG CYS B 280 ZN ZN B1336 1555 1555 2.09 LINK SG CYS B 283 ZN ZN B1336 1555 1555 2.13 LINK SG CYS B 296 ZN ZN B1337 1555 1555 2.13 LINK SG CYS B 299 ZN ZN B1337 1555 1555 2.15 SITE 1 AC1 4 CYS A 259 CYS A 262 CYS A 280 CYS A 283 SITE 1 AC2 5 CYS A 274 CYS A 275 CYS A 296 THR A 298 SITE 2 AC2 5 CYS A 299 SITE 1 AC3 4 CYS B 259 CYS B 262 CYS B 280 CYS B 283 SITE 1 AC4 5 CYS B 274 CYS B 275 CYS B 296 THR B 298 SITE 2 AC4 5 CYS B 299 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