10 20 30 40 50 60 70 80 2JY6 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER SIGNALING PROTEIN 06-DEC-07 2JY6
TITLE SOLUTION STRUCTURE OF THE COMPLEX OF UBIQUITIN AND TITLE 2 UBIQUILIN 1 UBA DOMAIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: UBIQUILIN-1; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: PROTEIN LINKING IAP WITH CYTOSKELETON 1, PLIC-1, COMPND 9 HPLIC- 1; 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 GENE: UBI1, RPL40A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET4A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: UBQLN1, DA41, PLIC1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 20 EXPRESSION_SYSTEM_VECTOR: PGEX-4T1
KEYWDS UBIQUILIN, UBA, UBIQUITIN, COMPLEX, ALTERNATIVE SPLICING, KEYWDS 2 CYTOPLASM, NUCLEUS, PHOSPHOPROTEIN, PROTEASOME, SIGNALING KEYWDS 3 PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR D.ZHANG,S.RAASI,D.FUSHMAN
REVDAT 2 24-FEB-09 2JY6 1 VERSN REVDAT 1 18-MAR-08 2JY6 0
JRNL AUTH D.ZHANG,S.RAASI,D.FUSHMAN JRNL TITL AFFINITY MAKES THE DIFFERENCE: NONSELECTIVE JRNL TITL 2 INTERACTION OF THE UBA DOMAIN OF UBIQUILIN-1 WITH JRNL TITL 3 MONOMERIC UBIQUITIN AND POLYUBIQUITIN CHAINS JRNL REF J.MOL.BIOL. V. 377 162 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18241885 JRNL DOI 10.1016/J.JMB.2007.12.029
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK REMARK 3 AUTHORS : BONVIN, A. M. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2JY6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-07. REMARK 100 THE RCSB ID CODE IS RCSB100437.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296; 306 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 20 MM; 20 MM REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM SODIUM PHOSPHATE, 0.02% REMARK 210 SODIUM AZIDE, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC, 2D 1H-15N REMARK 210 IPAP HSQC, 15N R1 AND R2, 15N{ REMARK 210 1H} NOE, 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : HADDOCK REMARK 210 METHOD USED : SIMULATED ANNEALING, DISTANCE REMARK 210 GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 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),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 7 SER B 587 CB SER B 587 OG 0.449 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 7 ASP A 52 CB - CG - OD1 ANGL. DEV. = -42.0 DEGREES REMARK 500 7 ASP A 52 CB - CG - OD2 ANGL. DEV. = -72.2 DEGREES 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 GLU A 34 -77.70 -84.07 REMARK 500 1 PHE B 547 -24.23 74.99 REMARK 500 1 GLN B 548 -51.24 68.45 REMARK 500 1 ARG B 562 -62.78 -125.62 REMARK 500 1 SER B 586 -101.00 -154.75 REMARK 500 2 ASN A 60 95.91 65.51 REMARK 500 2 PHE B 547 -33.07 74.87 REMARK 500 2 GLN B 548 -45.69 71.10 REMARK 500 2 ARG B 562 -50.31 -133.72 REMARK 500 2 SER B 586 -87.47 -145.01 REMARK 500 3 GLU A 34 -70.36 -86.39 REMARK 500 3 ASN A 60 83.43 59.85 REMARK 500 3 PHE B 547 -31.18 73.99 REMARK 500 3 GLN B 548 -40.69 69.04 REMARK 500 3 ARG B 562 -50.53 -123.31 REMARK 500 3 SER B 586 -81.15 -153.46 REMARK 500 4 PHE B 547 -6.99 73.96 REMARK 500 4 GLN B 548 -63.28 65.37 REMARK 500 4 ARG B 562 -50.67 -129.47 REMARK 500 4 SER B 586 -78.83 -153.05 REMARK 500 5 ASN A 60 83.70 57.49 REMARK 500 5 PHE B 547 -20.62 73.16 REMARK 500 5 GLN B 548 -48.68 70.28 REMARK 500 5 SER B 586 -76.33 -140.20 REMARK 500 6 PHE B 547 -33.06 74.21 REMARK 500 6 GLN B 548 -33.59 70.79 REMARK 500 6 SER B 586 -158.04 -133.74 REMARK 500 7 PHE B 547 -17.24 75.22 REMARK 500 7 GLN B 548 -52.27 68.22 REMARK 500 7 SER B 586 -90.83 -149.04 REMARK 500 8 THR A 7 -145.10 -120.11 REMARK 500 8 ASN A 60 106.75 69.77 REMARK 500 8 PHE B 547 -7.34 71.74 REMARK 500 8 GLN B 548 -67.26 67.97 REMARK 500 8 ARG B 562 -50.86 -128.36 REMARK 500 9 ASN A 60 74.57 59.67 REMARK 500 9 PHE B 547 -37.87 74.93 REMARK 500 9 GLN B 548 -40.63 73.58 REMARK 500 10 PHE B 547 -21.62 75.24 REMARK 500 10 GLN B 548 -56.18 71.25 REMARK 500 10 ARG B 562 -58.72 -121.50 REMARK 500 REMARK 500 REMARK: NULL
REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JY5 RELATED DB: PDB
DBREF 2JY6 A 1 76 UNP Q96H31 Q96H31_HUMAN 14 89 DBREF 2JY6 B 541 586 UNP Q9UMX0 UBQL1_HUMAN 541 586
SEQADV 2JY6 GLY B 536 UNP Q9UMX0 EXPRESSION TAG SEQADV 2JY6 SER B 537 UNP Q9UMX0 EXPRESSION TAG SEQADV 2JY6 PRO B 538 UNP Q9UMX0 EXPRESSION TAG SEQADV 2JY6 GLU B 539 UNP Q9UMX0 EXPRESSION TAG SEQADV 2JY6 PHE B 540 UNP Q9UMX0 EXPRESSION TAG SEQADV 2JY6 SER B 587 UNP Q9UMX0 EXPRESSION TAG
SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 52 GLY SER PRO GLU PHE GLN ASN PRO GLU VAL ARG PHE GLN SEQRES 2 B 52 GLN GLN LEU GLU GLN LEU SER ALA MET GLY PHE LEU ASN SEQRES 3 B 52 ARG GLU ALA ASN LEU GLN ALA LEU ILE ALA THR GLY GLY SEQRES 4 B 52 ASP ILE ASN ALA ALA ILE GLU ARG LEU LEU GLY SER SER
HELIX 1 1 THR A 22 GLU A 34 1 13 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 GLN B 549 ALA B 556 1 8 HELIX 4 4 ARG B 562 GLY B 573 1 12 HELIX 5 5 ASP B 575 SER B 586 1 12
SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 THR A 7 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 THR A 66 LEU A 71 1 O LEU A 67 N PHE A 4 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 A 5 LYS A 48 LEU A 50 -1 O LEU A 50 N LEU A 43
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