10 20 30 40 50 60 70 80 2Z59 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PROTEIN TRANSPORT 01-JUL-07 2Z59
TITLE COMPLEX STRUCTURES OF MOUSE RPN13 (22-130AA) AND UBIQUITIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ADRM1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 22-130; COMPND 5 SYNONYM: PROTEASOME COMPONENT RPN13, ADHESION-REGULATING COMPND 6 MOLECULE 1, 110 KDA CELL MEMBRANE GLYCOPROTEIN, GP110, ARM- COMPND 7 1; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: UBIQUITIN; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: ADRM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PRSET; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: RPS27A, UBA80, UBCEP1; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PET
KEYWDS PROTEASOME, NMR, PH DOMAIN, PROTEIN TRANSPORT
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR X.CHEN,P.SCHREINER,M.GROLL,K.J.WALTERS
REVDAT 3 19-JAN-10 2Z59 1 JRNL REVDAT 2 24-FEB-09 2Z59 1 VERSN REVDAT 1 20-MAY-08 2Z59 0
JRNL AUTH P.SCHREINER,X.CHEN,K.HUSNJAK,L.RANDLES,N.ZHANG, JRNL AUTH 2 S.ELSASSER,D.FINLEY,I.DIKIC,K.J.WALTERS,M.GROLL JRNL TITL UBIQUITIN DOCKING AT THE PROTEASOME THROUGH A NOVEL JRNL TITL 2 PLECKSTRIN-HOMOLOGY DOMAIN INTERACTION. JRNL REF NATURE V. 453 548 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18497827 JRNL DOI 10.1038/NATURE06924
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK 1.3 REMARK 3 AUTHORS : CYRIL DOMINGUEZ, ROLF BOELENS, ALEXANDRE REMARK 3 M.J.J.BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRCTURES ARE BASED ON REMARK 3 INTERACTION DATA SUCH AS CHEMICAL SHIFT PERTURBATION DATA REMARK 3 RESULTING FROM NMR TITRATION EXPERIMENTS AND INTERMOLECULAR REMARK 3 NOE.
REMARK 4 REMARK 4 2Z59 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUL-07. REMARK 100 THE RCSB ID CODE IS RCSB027537.
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 : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6MM MMRPN13 U-15N, 13C; U- REMARK 210 70% 2H; 20MM PHOSPHATE BUFFER; REMARK 210 30MM NACL; 3MM DTT; 90% H2O, REMARK 210 10% D2O; 0.6MM MMRPN13 U-15N; REMARK 210 U-50% 2H; 20MM PHOSPHATE REMARK 210 BUFFER; 30MM NACL; 3MM DTT; REMARK 210 90% H2O, 10% D2O; 0.6MM REMARK 210 MMRPN13 U-15N, 13C; U-70% 2H; REMARK 210 0.6MM UBIQUITIN; 20MM REMARK 210 PHOSPHATE BUFFER; 30MM NACL; REMARK 210 3MM DTT; 90% H2O, 10% D2O; REMARK 210 0.4MM MMRPN13 U-15N; 20MM REMARK 210 PHOSPHATE BUFFER; 30MM NACL; REMARK 210 3MM DTT; 90% H2O, 10% D2O; REMARK 210 0.4MM UBIQUITIN U-15N; 20MM REMARK 210 PHOSPHATE BUFFER; 30MM NACL; REMARK 210 3MM DTT; 90% H2O, 10% D2O; REMARK 210 0.4MM MMRPN13 U-13C; 20MM REMARK 210 PHOSPHATE BUFFER; 30MM NACL; REMARK 210 3MM DTT; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCACB, HNCA/HN(CO)CA; 3D_15N REMARK 210 -SEPARATED_NOESY; HSQC REMARK 210 TITRATION REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2006, XEASY 1996, REMARK 210 HADDOCK 1.3 REMARK 210 METHOD USED : HIGH AMBIGUITY DRIVEN PROTEIN REMARK 210 -PROTEIN DOCKING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: 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 A 78 HZ2 LYS A 99 1.58 REMARK 500 HZ1 LYS A 30 OD1 ASP A 71 1.58 REMARK 500 HZ2 LYS B 11 OE2 GLU B 34 1.60 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 ASP A 78 -32.04 69.36 REMARK 500 1 GLN A 87 44.01 -91.99 REMARK 500 1 ALA B 46 44.73 70.30 REMARK 500 2 ALA B 46 62.70 63.56 REMARK 500 3 THR A 36 -3.02 -143.11 REMARK 500 3 GLU A 70 -75.12 -91.76 REMARK 500 3 ASP A 72 89.80 -161.73 REMARK 500 3 ASP A 78 -37.59 77.36 REMARK 500 3 ASP B 52 98.25 -63.92 REMARK 500 3 ARG B 74 -58.33 -132.82 REMARK 500 5 GLU A 70 -68.12 -92.24 REMARK 500 5 ASP A 78 -13.38 78.21 REMARK 500 5 GLN B 62 -165.45 -112.48 REMARK 500 6 LYS B 33 -72.75 -80.21 REMARK 500 6 GLN B 62 -164.19 -100.42 REMARK 500 7 LEU A 23 -78.31 -68.58 REMARK 500 7 THR A 36 3.05 -154.38 REMARK 500 7 ASP A 78 -13.73 77.49 REMARK 500 7 ASN A 129 -33.78 -130.64 REMARK 500 8 ASP A 78 -10.25 84.32 REMARK 500 9 ASP A 78 -38.44 72.11 REMARK 500 10 ALA B 46 70.54 65.54 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB REMARK 900 UBIQUITIN NMR STRUCTURE REMARK 900 RELATED ID: 2HTH RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR UBIQUITIN RECOGNITION BY THE HUMAN REMARK 900 EAP45/ESCRT-II GLUE DOMAIN REMARK 900 RELATED ID: 2R2Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MRPN13 PRU
DBREF 2Z59 A 22 130 UNP Q9JKV1 ADRM1_MOUSE 22 130
DBREF1 2Z59 B 1 76 UNP P62988
DBREF2 2Z59 B UBIQ_UBIQ_HUMAN 1 76
SEQRES 1 A 109 TYR LEU VAL GLU PHE ARG ALA GLY LYS MET SER LEU LYS SEQRES 2 A 109 GLY THR THR VAL THR PRO ASP LYS ARG LYS GLY LEU VAL SEQRES 3 A 109 TYR ILE GLN GLN THR ASP ASP SER LEU ILE HIS PHE CYS SEQRES 4 A 109 TRP LYS ASP ARG THR SER GLY THR VAL GLU ASP ASP LEU SEQRES 5 A 109 ILE ILE PHE PRO ASP ASP CYS GLU PHE LYS ARG VAL PRO SEQRES 6 A 109 GLN CYS PRO SER GLY ARG VAL TYR VAL LEU LYS PHE LYS SEQRES 7 A 109 ALA GLY SER LYS ARG LEU PHE PHE TRP MET GLN GLU PRO SEQRES 8 A 109 LYS THR ASP GLN ASP GLU GLU HIS CYS ARG LYS VAL ASN SEQRES 9 A 109 GLU CYS LEU ASN ASN 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
HELIX 1 1 LYS A 113 ASP A 115 5 3 HELIX 2 2 GLN A 116 ASN A 130 1 15 HELIX 3 3 THR B 22 GLU B 34 1 13 HELIX 4 4 PRO B 37 ASP B 39 5 3
SHEET 1 A 5 THR A 37 PRO A 40 0 SHEET 2 A 5 PHE A 26 LYS A 34 -1 N SER A 32 O THR A 39 SHEET 3 A 5 GLY A 45 GLN A 51 -1 O VAL A 47 N PHE A 26 SHEET 4 A 5 ILE A 57 ASP A 63 -1 O LYS A 62 N LEU A 46 SHEET 5 A 5 VAL A 69 ILE A 75 -1 O ILE A 75 N ILE A 57 SHEET 1 B 5 THR A 37 PRO A 40 0 SHEET 2 B 5 PHE A 26 LYS A 34 -1 N SER A 32 O THR A 39 SHEET 3 B 5 ARG A 104 MET A 109 -1 O TRP A 108 N GLY A 29 SHEET 4 B 5 VAL A 93 PHE A 98 -1 N TYR A 94 O PHE A 107 SHEET 5 B 5 CYS A 80 ARG A 84 -1 N LYS A 83 O VAL A 95 SHEET 1 C 4 THR B 12 GLU B 16 0 SHEET 2 C 4 GLN B 2 THR B 7 -1 N VAL B 5 O ILE B 13 SHEET 3 C 4 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 C 4 GLN B 41 ILE B 44 -1 N ARG B 42 O VAL B 70
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