HEADER PROTEIN BINDING 30-DEC-02 1NJ3 TITLE STRUCTURE AND UBIQUITIN INTERACTIONS OF THE CONSERVED NZF DOMAIN OF TITLE 2 NPL4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NPL4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NZF DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: NPL4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T KEYWDS NZF DOMAIN, NPL4, RUBREDOXIN KNUCKLE, BETA-RIBBON, ZINC-FINGER, KEYWDS 2 UBIQUITIN, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.WANG,S.L.ALAM,H.H.MEYER,M.PAYNE,T.L.STEMMLER,D.R.DAVIS, AUTHOR 2 W.I.SUNDQUIST REVDAT 4 22-NOV-17 1NJ3 1 REMARK REVDAT 3 24-FEB-09 1NJ3 1 VERSN REVDAT 2 01-MAR-05 1NJ3 1 JRNL REVDAT 1 22-APR-03 1NJ3 0 JRNL AUTH B.WANG,S.L.ALAM,H.H.MEYER,M.PAYNE,T.L.STEMMLER,D.R.DAVIS, JRNL AUTH 2 W.I.SUNDQUIST JRNL TITL STRUCTURE AND UBIQUITIN INTERACTIONS OF THE CONSERVED ZINC JRNL TITL 2 FINGER DOMAIN OF NPL4. JRNL REF J.BIOL.CHEM. V. 278 20225 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12644454 JRNL DOI 10.1074/JBC.M300459200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.H.MEYER,J.G.SHORTER,D.PAPPIN,G.WARREN REMARK 1 TITL A COMPLEX OF MAMMALIAN UFD1 AND NLP4 LINKS THE AAA-ATPASE, REMARK 1 TITL 2 P97, TO UBIQUITIN AND NUCLEAR TRANSPORT REMARK 1 REF EMBO J. V. 15 2181 2000 REMARK 1 REFN ISSN 0261-4189 REMARK 1 DOI 10.1093/EMBOJ/19.10.2181 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.H.MEYER,Y.WANG,G.WARREN REMARK 1 TITL DIRECT BINDING OF UBIQUITIN CONJUGATES BY THE MAMMALIAN P97 REMARK 1 TITL 2 ADAPTER COMPLEXES, P47 AND UFD1-NPL4 REMARK 1 REF EMBO J. V. 21 5645 2002 REMARK 1 REFN ISSN 0261-4189 REMARK 1 DOI 10.1093/EMBOJ/CDF579 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, DYANA 1.5 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE REMARK 3 -KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, REMARK 3 RICE, SIMONSON, WARREN (CNS), GUNTERT, P., REMARK 3 MUMENTHALER, C., WUTHRICH, K. (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 INITAL STRUCTURES FROM TORSION ANGLE DYNAMICS (DYANA) REMARK 3 WERE REGULARIZED WITH A GENTLE ANNELAING REMARK 3 PROTOCOL IN CNS REMARK 4 REMARK 4 1NJ3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1000017911. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 291 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 70 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM NPL4 NZF DOMAIN, U-15N,13C; REMARK 210 20 MM SODIUM PHOSPHATE, PH 5.5, REMARK 210 50MM NACL, 5 MM BME,90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCACB; HN(CA)CO; H(CCO)NH REMARK 210 -TOCSY; (H)C(CO)NH-TOCSY; 3D_13C- REMARK 210 SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 97, SPARKY 3.106 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS AND REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: 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 SER A 2 84.61 60.43 REMARK 500 1 THR A 3 -168.37 -129.26 REMARK 500 1 SER A 4 -80.62 -67.39 REMARK 500 1 HIS A 11 -59.68 -137.66 REMARK 500 1 THR A 13 41.87 73.48 REMARK 500 1 THR A 20 58.86 -93.82 REMARK 500 1 HIS A 22 -110.88 -72.65 REMARK 500 1 CYS A 23 152.11 174.45 REMARK 500 1 MET A 25 -62.34 -134.23 REMARK 500 1 SER A 27 35.49 96.17 REMARK 500 2 SER A 4 -77.64 -65.68 REMARK 500 2 HIS A 11 -57.32 -137.97 REMARK 500 2 THR A 13 37.29 81.99 REMARK 500 2 THR A 20 58.30 -93.78 REMARK 500 2 HIS A 22 -110.96 -72.82 REMARK 500 2 CYS A 23 156.36 175.36 REMARK 500 2 MET A 25 -59.83 -133.03 REMARK 500 2 SER A 27 35.42 96.58 REMARK 500 3 SER A 2 -70.65 68.03 REMARK 500 3 SER A 4 -68.89 -91.42 REMARK 500 3 HIS A 11 -60.26 -138.03 REMARK 500 3 THR A 13 42.10 73.44 REMARK 500 3 HIS A 22 -110.34 -71.45 REMARK 500 3 CYS A 23 147.72 173.71 REMARK 500 3 MET A 25 -63.27 -134.44 REMARK 500 3 SER A 27 35.50 96.93 REMARK 500 4 SER A 4 -76.30 -83.21 REMARK 500 4 HIS A 11 -58.93 -137.83 REMARK 500 4 THR A 13 37.64 81.52 REMARK 500 4 HIS A 22 -110.97 -72.29 REMARK 500 4 CYS A 23 154.99 174.93 REMARK 500 4 MET A 25 -60.20 -132.79 REMARK 500 4 SER A 27 35.53 96.86 REMARK 500 5 SER A 4 -74.44 -82.36 REMARK 500 5 HIS A 11 -59.26 -137.72 REMARK 500 5 THR A 13 37.39 82.00 REMARK 500 5 THR A 20 58.41 -93.68 REMARK 500 5 HIS A 22 -110.88 -72.54 REMARK 500 5 CYS A 23 155.08 175.27 REMARK 500 5 MET A 25 -61.16 -132.93 REMARK 500 5 SER A 27 35.49 97.28 REMARK 500 6 SER A 2 103.66 60.61 REMARK 500 6 SER A 4 -78.21 -69.02 REMARK 500 6 HIS A 11 -59.12 -137.42 REMARK 500 6 THR A 13 37.66 81.68 REMARK 500 6 THR A 20 59.08 -93.62 REMARK 500 6 HIS A 22 -110.70 -71.98 REMARK 500 6 CYS A 23 153.14 174.78 REMARK 500 6 MET A 25 -60.83 -132.65 REMARK 500 6 SER A 27 35.91 95.56 REMARK 500 REMARK 500 THIS ENTRY HAS 161 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 32 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 23 SG REMARK 620 2 CYS A 26 SG 105.7 REMARK 620 3 CYS A 12 SG 105.8 130.3 REMARK 620 4 CYS A 9 SG 101.2 106.0 104.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 32 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FHH RELATED DB: PDB REMARK 900 STRUCTURALLY RELATED TO REBREDOXIN REMARK 900 RELATED ID: 1DVB RELATED DB: PDB REMARK 900 STRUCTURALLY REALTED TO RUBRERYTHRIN DBREF 1NJ3 A 3 31 UNP Q9ES54 NPL4_RAT 580 608 SEQADV 1NJ3 GLY A 1 UNP Q9ES54 CLONING ARTIFACT SEQADV 1NJ3 SER A 2 UNP Q9ES54 CLONING ARTIFACT SEQRES 1 A 31 GLY SER THR SER ALA MET TRP ALA CYS GLN HIS CYS THR SEQRES 2 A 31 PHE MET ASN GLN PRO GLY THR GLY HIS CYS GLU MET CYS SEQRES 3 A 31 SER LEU PRO ARG THR HET ZN A 32 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ SHEET 1 A 2 TRP A 7 ALA A 8 0 SHEET 2 A 2 MET A 15 ASN A 16 -1 O ASN A 16 N TRP A 7 LINK ZN ZN A 32 SG CYS A 23 1555 1555 2.41 LINK ZN ZN A 32 SG CYS A 26 1555 1555 2.30 LINK ZN ZN A 32 SG CYS A 12 1555 1555 2.31 LINK ZN ZN A 32 SG CYS A 9 1555 1555 2.42 SITE 1 AC1 4 CYS A 9 CYS A 12 CYS A 23 CYS A 26 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