HEADER PROTEIN BINDING 04-SEP-08 2K8B TITLE SOLUTION STRUCTURE OF PLAA FAMILY UBIQUITIN BINDING DOMAIN (PFUC) CIS TITLE 2 ISOMER IN COMPLEX WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PHOSPHOLIPASE A-2-ACTIVATING PROTEIN; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: UNP RESIDUES 386-465; COMPND 9 SYNONYM: PLA2P, PLAP; 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: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-22B; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: PLAA, PLAP; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR: PET-32M KEYWDS UBIQUITIN IN COMPLEX WITH PFUC CIS ISOMER, CYTOPLASM, NUCLEUS, KEYWDS 2 PHOSPHOPROTEIN, UBL CONJUGATION, WD REPEAT, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Q.S.FU,C.J.ZHOU,H.C.GAO,D.H.LIN,H.Y.HU REVDAT 4 16-MAR-22 2K8B 1 REMARK REVDAT 3 28-JUL-09 2K8B 1 JRNL REVDAT 2 14-JUL-09 2K8B 1 JRNL REVDAT 1 05-MAY-09 2K8B 0 JRNL AUTH Q.S.FU,C.J.ZHOU,H.C.GAO,Y.J.JIANG,Z.R.ZHOU,J.HONG,W.M.YAO, JRNL AUTH 2 A.X.SONG,D.H.LIN,H.Y.HU JRNL TITL STRUCTURAL BASIS FOR UBIQUITIN RECOGNITION BY A NOVEL DOMAIN JRNL TITL 2 FROM HUMAN PHOSPHOLIPASE A2-ACTIVATING PROTEIN. JRNL REF J.BIOL.CHEM. V. 284 19043 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19423704 JRNL DOI 10.1074/JBC.M109.009126 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE CALCULATED WITH REMARK 3 HADDOCK BY NMR RESTRAINT-GUIDED DOCKING REMARK 4 REMARK 4 2K8B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000100802. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2 MM UBIQUITIN, 90% H2O, 10% REMARK 210 D2O; 0.2 MM PFUC_CIS, 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : 10 STRUCTURES FOR LOWEST 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: DIMERIC 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 108 HZ1 LYS B 112 1.57 REMARK 500 HZ3 LYS B 56 OD1 ASP B 65 1.58 REMARK 500 HZ1 LYS A 6 OD1 ASP B 71 1.58 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 ASN B 50 26.68 -145.77 REMARK 500 1 GLN B 51 35.23 -90.34 REMARK 500 1 GLN B 52 59.58 -90.44 REMARK 500 1 GLU B 60 -67.74 65.38 REMARK 500 1 ASN B 73 -42.98 177.66 REMARK 500 1 SER B 86 49.19 -108.08 REMARK 500 1 ASP B 101 79.16 62.56 REMARK 500 1 MET B 122 33.55 -92.76 REMARK 500 1 LEU B 123 -45.00 -141.67 REMARK 500 1 LEU B 125 -151.34 60.32 REMARK 500 2 ASN B 50 11.71 -154.52 REMARK 500 2 GLU B 60 -75.88 64.14 REMARK 500 2 ASP B 65 -71.66 -67.83 REMARK 500 2 ASN B 73 -44.01 177.08 REMARK 500 2 GLN B 121 -88.73 40.89 REMARK 500 2 LEU B 123 -74.46 -128.57 REMARK 500 2 LEU B 125 -146.97 -99.95 REMARK 500 3 GLU A 34 -72.17 -109.66 REMARK 500 3 ALA A 46 19.38 59.90 REMARK 500 3 GLN B 51 36.44 -78.19 REMARK 500 3 GLU B 60 -92.04 57.23 REMARK 500 3 ASP B 65 -71.56 -60.86 REMARK 500 3 ASN B 73 -45.96 -175.68 REMARK 500 3 MET B 122 35.75 -90.66 REMARK 500 3 LEU B 123 -53.89 -134.75 REMARK 500 3 LEU B 125 -155.36 66.18 REMARK 500 4 ASN B 50 23.84 -151.13 REMARK 500 4 GLN B 51 30.79 -94.17 REMARK 500 4 GLU B 60 -82.10 61.86 REMARK 500 4 ASP B 65 -78.54 -63.66 REMARK 500 4 ASN B 73 -50.52 -174.21 REMARK 500 4 SER B 86 59.65 -109.83 REMARK 500 4 ASP B 101 70.91 59.96 REMARK 500 4 LEU B 125 -159.64 59.37 REMARK 500 5 THR A 7 -166.03 -79.33 REMARK 500 5 LYS A 33 -73.33 -81.49 REMARK 500 5 GLU B 60 -84.69 60.45 REMARK 500 5 ASP B 65 -70.08 -63.60 REMARK 500 5 ASN B 73 -59.19 -179.91 REMARK 500 5 SER B 86 31.53 -99.45 REMARK 500 5 ASP B 87 -162.61 -116.05 REMARK 500 5 LEU B 125 -141.45 59.81 REMARK 500 6 GLU A 34 -162.83 -105.17 REMARK 500 6 GLU B 60 -82.16 62.70 REMARK 500 6 ASN B 73 -49.32 -176.46 REMARK 500 6 ASP B 101 78.21 58.38 REMARK 500 6 LEU B 125 -148.50 65.45 REMARK 500 7 LEU A 71 -165.46 -101.17 REMARK 500 7 GLN B 52 102.61 72.43 REMARK 500 7 GLU B 60 17.84 54.81 REMARK 500 REMARK 500 THIS ENTRY HAS 82 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K89 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF UBIQUITIN-BINDING DOMAIN PLAA (PFUC, GLY76- REMARK 900 PRO77 CIS ISOMER) REMARK 900 RELATED ID: 2K8A RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF UBIQUITIN-BINDING DOMAIN PLAA (PFUC, GLY76- REMARK 900 PRO77 TRANS ISOMER) REMARK 900 RELATED ID: 2K8C RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF PLAA FAMILY UBIQUITIN BINDING DOMAIN (PFUC) REMARK 900 TRANS ISOMER IN COMPLEX WITH UBIQUITIN DBREF 2K8B A 1 76 UNP P62988 UBIQ_HUMAN 1 76 DBREF 2K8B B 49 128 UNP Q9Y263 PLAP_HUMAN 386 465 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 80 ALA ASN GLN GLN THR SER GLY LYS VAL LEU TYR GLU GLY SEQRES 2 B 80 LYS GLU PHE ASP TYR VAL PHE SER ILE ASP VAL ASN GLU SEQRES 3 B 80 GLY GLY PRO SER TYR LYS LEU PRO TYR ASN THR SER ASP SEQRES 4 B 80 ASP PRO TRP LEU THR ALA TYR ASN PHE LEU GLN LYS ASN SEQRES 5 B 80 ASP LEU ASN PRO MET PHE LEU ASP GLN VAL ALA LYS PHE SEQRES 6 B 80 ILE ILE ASP ASN THR LYS GLY GLN MET LEU GLY LEU GLY SEQRES 7 B 80 ASN PRO HELIX 1 1 THR A 22 GLU A 34 1 13 HELIX 2 2 ASP B 88 ASP B 101 1 14 HELIX 3 3 PRO B 104 GLY B 120 1 17 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 LYS A 6 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 B 2 VAL B 57 TYR B 59 0 SHEET 2 B 2 LYS B 62 PHE B 64 -1 O LYS B 62 N TYR B 59 SHEET 1 C 2 TYR B 66 ILE B 70 0 SHEET 2 C 2 TYR B 79 TYR B 83 -1 O TYR B 83 N TYR B 66 CISPEP 1 GLY B 76 PRO B 77 1 -0.43 CISPEP 2 GLY B 76 PRO B 77 2 -0.14 CISPEP 3 GLY B 76 PRO B 77 3 -1.20 CISPEP 4 GLY B 76 PRO B 77 4 -0.83 CISPEP 5 GLY B 76 PRO B 77 5 -0.21 CISPEP 6 GLY B 76 PRO B 77 6 -0.20 CISPEP 7 GLY B 76 PRO B 77 7 -0.75 CISPEP 8 GLY B 76 PRO B 77 8 0.64 CISPEP 9 GLY B 76 PRO B 77 9 -0.14 CISPEP 10 GLY B 76 PRO B 77 10 -0.27 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