10 20 30 40 50 60 70 80 1ZO6 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PROTEIN TURNOVER/SIGNALING PROTEIN 12-MAY-05 1ZO6
TITLE NMR BASED MODEL OF LYS48-LINKED DI-UBIQUITIN COMPLEX WITH C- TITLE 2 TERMINAL UBA DOMAIN OF HHR23A
COMPND MOL_ID: 1; COMPND 2 MOLECULE: UV EXCISION REPAIR PROTEIN RAD23 HOMOLOG A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 315-363; COMPND 5 SYNONYM: HHR23A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UBIQUITIN; COMPND 9 CHAIN: B, C; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: ISOPEPTIDE BOND BETWEEN GLY76C AND LYS48B
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: RAD23A; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL-21 DE3(PLYSS); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL-21 DE3(PLYSS)
KEYWDS DI-UBIQUITIN, LYS48-LINKED POLYUBIQUITIN, UBA2, HHR23A
EXPDTA THEORETICAL MODEL
AUTHOR R.VARADAN,M.ASSFALG,S.RAASI,C.PICKART,D.FUSHMAN
REVDAT 2 21-JUN-05 1ZO6 1 JRNL REVDAT 1 14-JUN-05 1ZO6 0
JRNL AUTH R.VARADAN,M.ASSFALG,S.RAASI,C.PICKART,D.FUSHMAN JRNL TITL STRUCTURAL DETERMINANTS FOR SELECTIVE RECOGNITION JRNL TITL 2 OF A LYS48-LINKED POLYUBIQUITIN CHAIN BY A UBA JRNL TITL 3 DOMAIN JRNL REF MOL. CELL V. 18 687 2005 JRNL REFN ASTM MOCEFL US ISSN 1097-2765
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK/TRIDOCK REMARK 3 AUTHORS : DOMINGUEZ,BOELENS,BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT IS DONE IN EXPLICIT REMARK 3 SOLVENT. REFINEMENT AND STRUCTURE CALCULATION DETAILS CAN BE REMARK 3 FOUND IN DOMINGUEZ ET AL, JACS 2003, 125, 173
REMARK 4 REMARK 4 1ZO6 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-2005. REMARK 100 THE RCSB ID CODE IS RCSB032946.
REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: SAMPLE: LYS48-LINKED UB2+UBA,PHOSPHATE BUFFER IN 93% REMARK 220 WATER/7% D20. THE STRUCTURE WAS DETERMINED WITH HADDOCK/ REMARK 220 TRIDOCK USING CHEMICAL SHIFT PERTURBATION DATA AS REMARK 220 AMBIGUOUS INTERACTION RESTRAINTS AND NOE DATA AS REMARK 220 UNAMBIGUOUS INTERACTION RESTRAINTS. REFINEMENT IS DONE REMARK 220 IN EXPLICIT SOLVENT. REFINEMENT AND STRUCTURE REMARK 220 CALCULATION DETAILS CAN BE FOUND IN DOMINGUEZ ET AL, REMARK 220 JACS 2003, 125, 173.
REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.
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 1 GLY A 310 REMARK 465 1 SER A 311 REMARK 465 1 ALA A 312 REMARK 465 1 ALA A 313 REMARK 465 1 ALA A 314 REMARK 465 1 GLN A 315 REMARK 465 1 VAL A 316 REMARK 465 1 THR A 317 REMARK 465 1 PRO A 318 REMARK 465 2 GLY A 310 REMARK 465 2 SER A 311 REMARK 465 2 ALA A 312 REMARK 465 2 ALA A 313 REMARK 465 2 ALA A 314 REMARK 465 2 GLN A 315 REMARK 465 2 VAL A 316 REMARK 465 2 THR A 317 REMARK 465 2 PRO A 318 REMARK 465 3 GLY A 310 REMARK 465 3 SER A 311 REMARK 465 3 ALA A 312 REMARK 465 3 ALA A 313 REMARK 465 3 ALA A 314 REMARK 465 3 GLN A 315 REMARK 465 3 VAL A 316 REMARK 465 3 THR A 317 REMARK 465 3 PRO A 318 REMARK 465 4 GLY A 310 REMARK 465 4 SER A 311 REMARK 465 4 ALA A 312 REMARK 465 4 ALA A 313 REMARK 465 4 ALA A 314 REMARK 465 4 GLN A 315 REMARK 465 4 VAL A 316 REMARK 465 4 THR A 317 REMARK 465 4 PRO A 318 REMARK 465 5 GLY A 310 REMARK 465 5 SER A 311 REMARK 465 5 ALA A 312 REMARK 465 5 ALA A 313 REMARK 465 5 ALA A 314 REMARK 465 5 GLN A 315 REMARK 465 5 VAL A 316 REMARK 465 5 THR A 317 REMARK 465 5 PRO A 318 REMARK 465 6 GLY A 310 REMARK 465 6 SER A 311 REMARK 465 6 ALA A 312 REMARK 465 6 ALA A 313 REMARK 465 6 ALA A 314 REMARK 465 6 GLN A 315 REMARK 465 6 VAL A 316 REMARK 465 6 THR A 317 REMARK 465 6 PRO A 318 REMARK 465 7 GLY A 310 REMARK 465 7 SER A 311 REMARK 465 7 ALA A 312 REMARK 465 7 ALA A 313 REMARK 465 7 ALA A 314 REMARK 465 7 GLN A 315 REMARK 465 7 VAL A 316 REMARK 465 7 THR A 317 REMARK 465 7 PRO A 318 REMARK 465 8 GLY A 310 REMARK 465 8 SER A 311 REMARK 465 8 ALA A 312 REMARK 465 8 ALA A 313 REMARK 465 8 ALA A 314 REMARK 465 8 GLN A 315 REMARK 465 8 VAL A 316 REMARK 465 8 THR A 317 REMARK 465 8 PRO A 318 REMARK 465 9 GLY A 310 REMARK 465 9 SER A 311 REMARK 465 9 ALA A 312 REMARK 465 9 ALA A 313 REMARK 465 9 ALA A 314 REMARK 465 9 GLN A 315 REMARK 465 9 VAL A 316 REMARK 465 9 THR A 317 REMARK 465 9 PRO A 318 REMARK 465 10 GLY A 310 REMARK 465 10 SER A 311 REMARK 465 10 ALA A 312 REMARK 465 10 ALA A 313 REMARK 465 10 ALA A 314 REMARK 465 10 GLN A 315 REMARK 465 10 VAL A 316 REMARK 465 10 THR A 317 REMARK 465 10 PRO A 318
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 3 GLU A 363 CA GLU A 363 CB 0.021 REMARK 500 7 GLU A 363 N GLU A 363 CA 0.020 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 3 LEU B 67 N - CA - C ANGL. DEV. = -3.5 DEGREES REMARK 500 5 LEU B 67 N - CA - C ANGL. DEV. = -3.2 DEGREES REMARK 500 6 LEU B 67 N - CA - C ANGL. DEV. = -3.4 DEGREES REMARK 500 6 VAL B 70 N - CA - C ANGL. DEV. = -3.3 DEGREES REMARK 500 9 LEU B 67 N - CA - C ANGL. DEV. = -3.2 DEGREES REMARK 500 10 GLU A 363 C - N - CA ANGL. DEV. = 3.2 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 10 ALA C 46 -42.15 71.86
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AAR RELATED DB: PDB REMARK 900 LYS48-LINKED UB2 REMARK 900 RELATED ID: 1DV0 RELATED DB: PDB REMARK 900 C-TERMINAL UBA DOMAIN OF HHR23A
DBREF 1ZO6 A 315 363 UNP P54725 RD23A_HUMAN 315 363 DBREF 1ZO6 B 1 76 UNP P62988 UBIQ_HUMAN 1 76 DBREF 1ZO6 C 1 76 UNP P62988 UBIQ_HUMAN 1 76
SEQADV 1ZO6 GLY A 310 UNP P54725 CLONING ARTIFACT SEQADV 1ZO6 SER A 311 UNP P54725 CLONING ARTIFACT SEQADV 1ZO6 ALA A 312 UNP P54725 CLONING ARTIFACT SEQADV 1ZO6 ALA A 313 UNP P54725 CLONING ARTIFACT SEQADV 1ZO6 ALA A 314 UNP P54725 CLONING ARTIFACT
SEQRES 1 A 54 GLY SER ALA ALA ALA GLN VAL THR PRO GLN GLU LYS GLU SEQRES 2 A 54 ALA ILE GLU ARG LEU LYS ALA LEU GLY PHE PRO GLU SER SEQRES 3 A 54 LEU VAL ILE GLN ALA TYR PHE ALA CYS GLU LYS ASN GLU SEQRES 4 A 54 ASN LEU ALA ALA ASN PHE LEU LEU SER GLN ASN PHE ASP SEQRES 5 A 54 ASP GLU SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY
HELIX 1 1 LYS A 321 ALA A 329 1 9 HELIX 2 2 GLU A 334 ALA A 343 1 10 HELIX 3 3 GLU A 348 LEU A 356 1 9 HELIX 4 1 THR B 22 GLU B 34 1 13 HELIX 5 2 PRO B 37 ASP B 39 5 3 HELIX 6 3 LEU B 56 ASN B 60 5 5 HELIX 7 4 THR C 22 GLU C 34 1 13 HELIX 8 5 PRO C 37 ASP C 39 5 3 HELIX 9 6 LEU C 56 ASN C 60 5 5
SHEET 1 AA 5 THR B 12 GLU B 16 0 SHEET 2 AA 5 GLN B 2 THR B 7 -1 O ILE B 3 N LEU B 15 SHEET 3 AA 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 AA 5 GLN B 41 PHE B 45 -1 O ARG B 42 N VAL B 70 SHEET 5 AA 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 BA 5 THR C 12 GLU C 16 0 SHEET 2 BA 5 GLN C 2 THR C 7 -1 O ILE C 3 N LEU C 15 SHEET 3 BA 5 THR C 66 LEU C 71 1 O LEU C 67 N LYS C 6 SHEET 4 BA 5 GLN C 41 PHE C 45 -1 O ARG C 42 N VAL C 70 SHEET 5 BA 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45
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