HEADER 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 MOLECULE 1, COMPND 6 110 KDA CELL MEMBRANE GLYCOPROTEIN, GP110, ARM-1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBIQUITIN; COMPND 10 CHAIN: B; COMPND 11 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, PH DOMAIN, PROTEIN TRANSPORT EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR X.CHEN,P.SCHREINER,M.GROLL,K.J.WALTERS REVDAT 4 16-MAR-22 2Z59 1 REMARK 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,S.ELSASSER, JRNL AUTH 2 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2006, HADDOCK 1.3 REMARK 3 AUTHORS : FRANK DELAGLIO, STEPHAN GRZESIEK, GUANG ZHU, REMARK 3 GEERTEN W. VUISTER, JOHN PFEIFER AND AD BAX REMARK 3 (NMRPIPE), CYRIL DOMINGUEZ, ROLF BOELENS, REMARK 3 ALEXANDRE M.J.J.BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRCTURES ARE BASED ON INTERACTION REMARK 3 DATA SUCH AS CHEMICAL SHIFT PERTURBATION DATA RESULTING FROM NMR REMARK 3 TITRATION EXPERIMENTS AND INTERMOLECULAR 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 DEPOSITION ID IS D_1000027537. 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-70% REMARK 210 2H; 20MM PHOSPHATE BUFFER; 30MM REMARK 210 NACL; 3MM DTT; 90% H2O, 10% D2O; REMARK 210 0.6MM MMRPN13 U-15N; U-50% 2H; REMARK 210 20MM PHOSPHATE BUFFER; 30MM NACL; REMARK 210 3MM DTT; 90% H2O, 10% D2O; REMARK 210 0.6MM MMRPN13 U-15N, 13C; U-70% REMARK 210 2H; 0.6MM UBIQUITIN; 20MM REMARK 210 PHOSPHATE BUFFER; 30MM NACL; 3MM REMARK 210 DTT; 90% H2O, 10% D2O; 0.4MM REMARK 210 MMRPN13 U-15N; 20MM PHOSPHATE REMARK 210 BUFFER; 30MM NACL; 3MM DTT; 90% REMARK 210 H2O, 10% D2O; 0.4MM UBIQUITIN U- REMARK 210 15N; 20MM PHOSPHATE BUFFER; 30MM REMARK 210 NACL; 3MM DTT; 90% H2O, 10% D2O; REMARK 210 0.4MM MMRPN13 U-13C; 20MM REMARK 210 PHOSPHATE BUFFER; 30MM NACL; 3MM REMARK 210 DTT; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCACB, HNCA/HN(CO)CA; 3D_15N REMARK 210 -SEPARATED_NOESY; HSQC 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 : XEASY 1996, 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 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 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 EAP45/ESCRT- REMARK 900 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 UBIQ_UBIQ_HUMAN DBREF2 2Z59 B P62988 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 MODEL 1