HEADER TRANSPORT PROTEIN 16-APR-07 2PJH TITLE STRCTURAL MODEL OF THE P97 N DOMAIN- NPL4 UBD COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR PROTEIN LOCALIZATION PROTEIN 4 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N DOMAIN (RESIDUES 1-80); COMPND 5 SYNONYM: PROTEIN NPL4; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UBD (RESIDUES 21-213); COMPND 11 SYNONYM: TER ATPASE, 15S MG2+, - ATPASE P97 SUBUNIT, VALOSIN- COMPND 12 CONTAINING PROTEIN, VCP; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: P97; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 GENE: NPL4; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS P97, UFD1, NPL4, AAA, ATPASE, PROTEIN BINDING, TRANSPORT PROTEIN EXPDTA SOLUTION NMR AUTHOR R.ISAACSON,V.E.PYE,S.SIMPSON,H.H.MEYER,X.ZHANG,P.FREEMONT REVDAT 5 22-MAY-24 2PJH 1 REMARK REVDAT 4 16-MAR-22 2PJH 1 REMARK REVDAT 3 24-FEB-09 2PJH 1 VERSN REVDAT 2 30-OCT-07 2PJH 1 JRNL REVDAT 1 08-MAY-07 2PJH 0 JRNL AUTH R.L.ISAACSON,V.E.PYE,P.SIMPSON,H.H.MEYER,X.ZHANG, JRNL AUTH 2 P.S.FREEMONT,S.MATTHEWS JRNL TITL DETAILED STRUCTURAL INSIGHTS INTO THE P97-NPL4-UFD1 JRNL TITL 2 INTERFACE. JRNL REF J.BIOL.CHEM. V. 282 21361 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17491009 JRNL DOI 10.1074/JBC.M610069200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK 1.3, HADDOCK 1.3 REMARK 3 AUTHORS : BONVIN (HADDOCK), BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CHEMICAL SHIFT BASED DOCKING REMARK 4 REMARK 4 2PJH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000042444. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 125MM NACL REMARK 210 PRESSURE : ATOMOSPHERIC ATM REMARK 210 SAMPLE CONTENTS : 15N LABELLED P97 N DOMAIN IN REMARK 210 COMPLEX WITH NPL4 UBD; 15N REMARK 210 LABELLED NPL4 UBD IN COMPLEX REMARK 210 WITH P97 N DOMAIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : HADDOCK - REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: DATA WAS NOT AVAILABLE TO CORRECT THE LARGE RMS DEVIATIONS REMARK 210 IN SER B 73 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 PHE A 78 REMARK 465 PRO A 79 REMARK 465 SER A 80 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 HE21 GLN A 10 HH TYR B 110 1.04 REMARK 500 OE1 GLU B 30 HH22 ARG B 89 1.57 REMARK 500 OE1 GLU B 66 HH12 ARG B 147 1.58 REMARK 500 HZ2 LYS A 52 OD1 ASP B 179 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 SER B 73 CB SER B 73 OG 0.600 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 ASP A 73 CB - CG - OD1 ANGL. DEV. = -17.3 DEGREES REMARK 500 ASP A 73 CB - CG - OD2 ANGL. DEV. = -49.1 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 ARG A 50 -151.97 -81.57 REMARK 500 THR A 57 -46.10 70.73 REMARK 500 LEU A 64 -151.79 -84.55 REMARK 500 LYS A 68 91.34 63.93 REMARK 500 ARG B 22 99.16 70.30 REMARK 500 GLN B 50 64.35 60.59 REMARK 500 PHE B 52 -146.77 -93.16 REMARK 500 ARG B 53 -87.33 -82.48 REMARK 500 ARG B 113 128.07 -170.73 REMARK 500 LEU B 135 48.57 -79.28 REMARK 500 LYS B 136 -57.25 -157.08 REMARK 500 MET B 158 -64.97 71.62 REMARK 500 CYS B 209 97.01 -69.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASP A 73 0.24 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2PJH A 1 80 UNP P60670 NPL4_MOUSE 1 80 DBREF 2PJH B 21 213 UNP Q01853 TERA_MOUSE 21 213 SEQRES 1 A 80 MET ALA GLU SER ILE ILE ILE ARG VAL GLN SER PRO ASP SEQRES 2 A 80 GLY VAL LYS ARG ILE THR ALA THR LYS ARG GLU THR ALA SEQRES 3 A 80 ALA THR PHE LEU LYS LYS VAL ALA LYS GLU PHE GLY PHE SEQRES 4 A 80 GLN ASN ASN GLY PHE SER VAL TYR ILE ASN ARG ASN LYS SEQRES 5 A 80 THR GLY GLU ILE THR ALA SER SER SER LYS SER LEU HIS SEQRES 6 A 80 LEU LEU LYS ILE LYS HIS GLY ASP LEU LEU PHE LEU PHE SEQRES 7 A 80 PRO SER SEQRES 1 B 193 ASN ARG PRO ASN ARG LEU ILE VAL ASP GLU ALA ILE ASN SEQRES 2 B 193 GLU ASP ASN SER VAL VAL SER LEU SER GLN PRO LYS MET SEQRES 3 B 193 ASP GLU LEU GLN LEU PHE ARG GLY ASP THR VAL LEU LEU SEQRES 4 B 193 LYS GLY LYS LYS ARG ARG GLU ALA VAL CYS ILE VAL LEU SEQRES 5 B 193 SER ASP ASP THR CYS SER ASP GLU LYS ILE ARG MET ASN SEQRES 6 B 193 ARG VAL VAL ARG ASN ASN LEU ARG VAL ARG LEU GLY ASP SEQRES 7 B 193 VAL ILE SER ILE GLN PRO CYS PRO ASP VAL LYS TYR GLY SEQRES 8 B 193 LYS ARG ILE HIS VAL LEU PRO ILE ASP ASP THR VAL GLU SEQRES 9 B 193 GLY ILE THR GLY ASN LEU PHE GLU VAL TYR LEU LYS PRO SEQRES 10 B 193 TYR PHE LEU GLU ALA TYR ARG PRO ILE ARG LYS GLY ASP SEQRES 11 B 193 ILE PHE LEU VAL ARG GLY GLY MET ARG ALA VAL GLU PHE SEQRES 12 B 193 LYS VAL VAL GLU THR ASP PRO SER PRO TYR CYS ILE VAL SEQRES 13 B 193 ALA PRO ASP THR VAL ILE HIS CYS GLU GLY GLU PRO ILE SEQRES 14 B 193 LYS ARG GLU ASP GLU GLU GLU SER LEU ASN GLU VAL GLY SEQRES 15 B 193 TYR ASP ASP VAL GLY GLY CYS ARG LYS GLN LEU HELIX 1 1 THR A 25 PHE A 37 1 13 HELIX 2 2 ASN A 51 ILE A 56 5 6 HELIX 3 3 SER B 42 LEU B 49 1 8 HELIX 4 4 ASN B 85 LEU B 92 1 8 HELIX 5 5 ASP B 120 VAL B 123 5 4 HELIX 6 6 GLY B 202 VAL B 206 5 5 SHEET 1 A 4 LEU A 75 PHE A 76 0 SHEET 2 A 4 ARG A 8 GLN A 10 1 N GLN A 10 O LEU A 75 SHEET 3 A 4 GLY A 14 ARG A 17 -1 O LYS A 16 N VAL A 9 SHEET 4 A 4 VAL B 108 LYS B 109 -1 O VAL B 108 N VAL A 15 SHEET 1 B 7 ARG B 25 ASP B 29 0 SHEET 2 B 7 LYS B 81 MET B 84 1 O ILE B 82 N ASP B 29 SHEET 3 B 7 VAL B 38 LEU B 41 -1 N SER B 40 O ARG B 83 SHEET 4 B 7 GLU B 66 SER B 73 1 O ILE B 70 N VAL B 39 SHEET 5 B 7 THR B 56 LYS B 60 -1 N LEU B 59 O ALA B 67 SHEET 6 B 7 VAL B 99 PRO B 104 -1 O SER B 101 N LYS B 60 SHEET 7 B 7 ARG B 25 ASP B 29 -1 N LEU B 26 O ILE B 100 SHEET 1 C 4 ILE B 151 VAL B 154 0 SHEET 2 C 4 VAL B 161 THR B 168 -1 O VAL B 161 N VAL B 154 SHEET 3 C 4 ILE B 114 PRO B 118 -1 N HIS B 115 O GLU B 167 SHEET 4 C 4 ILE B 182 HIS B 183 1 O HIS B 183 N ILE B 114 SHEET 1 D 2 PRO B 145 ARG B 147 0 SHEET 2 D 2 TYR B 173 ILE B 175 -1 O CYS B 174 N ILE B 146 CISPEP 1 SER B 171 PRO B 172 0 -0.29 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