10 20 30 40 50 60 70 80 1NJ3 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PROTEIN BINDING 30-DEC-02 1NJ3
TITLE STRUCTURE AND UBIQUITIN INTERACTIONS OF THE CONSERVED NZF TITLE 2 DOMAIN OF 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- KEYWDS 2 FINGER, 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 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, JRNL AUTH 2 D.R.DAVIS,W.I.SUNDQUIST JRNL TITL STRUCTURE AND UBIQUITIN INTERACTIONS OF THE JRNL TITL 2 CONSERVED ZINC 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 REMARK 1 TITL 2 AAA-ATPASE, 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 REMARK 1 TITL 2 MAMMALIAN P97 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, REMARK 3 READ, RICE, SIMONSON, WARREN (CNS), GUNTERT, P., REMARK 3 MUMENTHALER, C., WUTHRICH, K. (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITAL STRUCTURES FROM TORSION ANGLE REMARK 3 DYNAMICS (DYANA) 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 13-JAN-03. REMARK 100 THE RCSB ID CODE IS RCSB017911.
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, REMARK 210 13C; 20 MM SODIUM PHOSPHATE, REMARK 210 PH 5.5, 50MM NACL, 5 MM BME, REMARK 210 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCACB, HN(CA)CO, H(CCO)NH- REMARK 210 TOCSY, (H)C(CO)NH-TOCSY, 3D_ REMARK 210 13C-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, REMARK 210 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: 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 7 SER A 2 92.88 60.68 REMARK 500 7 SER A 4 -79.67 -74.63 REMARK 500 7 HIS A 11 -59.93 -137.78 REMARK 500 7 THR A 13 42.36 73.23 REMARK 500 7 HIS A 22 -110.24 -71.95 REMARK 500 7 CYS A 23 147.13 173.73 REMARK 500 7 MET A 25 -63.54 -134.36 REMARK 500 7 SER A 27 35.36 97.09 REMARK 500 8 THR A 3 111.05 60.79 REMARK 500 8 SER A 4 -75.16 -61.24 REMARK 500 8 HIS A 11 -59.44 -137.74 REMARK 500 8 THR A 13 37.59 81.96 REMARK 500 8 HIS A 22 -110.78 -71.94 REMARK 500 8 CYS A 23 153.71 174.79 REMARK 500 8 MET A 25 -61.82 -132.94 REMARK 500 8 SER A 27 35.26 98.22 REMARK 500 9 THR A 3 139.75 63.48 REMARK 500 9 SER A 4 -75.91 -82.27 REMARK 500 9 HIS A 11 -59.34 -137.82 REMARK 500 9 THR A 13 37.58 81.93 REMARK 500 9 HIS A 22 -110.71 -72.15 REMARK 500 9 CYS A 23 153.69 174.79 REMARK 500 9 MET A 25 -61.91 -132.98 REMARK 500 9 SER A 27 35.12 98.40 REMARK 500 10 SER A 4 -76.99 -86.51 REMARK 500 10 HIS A 11 -59.03 -138.49 REMARK 500 10 THR A 13 37.88 81.72 REMARK 500 10 HIS A 22 -110.30 -72.37 REMARK 500 10 CYS A 23 148.46 173.97 REMARK 500 10 MET A 25 -61.55 -133.57 REMARK 500 10 SER A 27 35.10 98.46 REMARK 500 11 SER A 2 89.13 -60.18 REMARK 500 11 THR A 3 115.82 -163.87 REMARK 500 11 SER A 4 -166.53 -60.17 REMARK 500 11 HIS A 11 -59.72 -137.57 REMARK 500 11 THR A 13 38.41 80.64 REMARK 500 11 HIS A 22 -109.31 -70.62 REMARK 500 11 CYS A 23 150.31 173.76 REMARK 500 11 MET A 25 -60.57 -133.01 REMARK 500 11 SER A 27 35.98 95.51 REMARK 500 12 SER A 4 -76.86 -91.84 REMARK 500 12 HIS A 11 -58.90 -138.07 REMARK 500 12 THR A 13 38.15 81.38 REMARK 500 12 HIS A 22 -110.42 -72.13 REMARK 500 12 CYS A 23 148.02 173.89 REMARK 500 12 MET A 25 -61.49 -133.67 REMARK 500 12 SER A 27 35.13 98.38 REMARK 500 13 SER A 4 -71.34 -147.42 REMARK 500 13 HIS A 11 -58.44 -138.12 REMARK 500 13 THR A 13 37.31 82.38 REMARK 500 13 HIS A 22 -110.85 -72.24 REMARK 500 13 CYS A 23 153.28 174.77 REMARK 500 13 MET A 25 -61.05 -132.81 REMARK 500 13 SER A 27 36.26 96.02 REMARK 500 14 SER A 4 -76.47 -85.17 REMARK 500 14 HIS A 11 -59.37 -137.69 REMARK 500 14 THR A 13 38.30 80.92 REMARK 500 14 HIS A 22 -110.40 -71.24 REMARK 500 14 CYS A 23 148.50 173.81 REMARK 500 14 MET A 25 -61.18 -133.53 REMARK 500 14 SER A 27 36.18 96.82 REMARK 500 15 SER A 2 109.14 60.47 REMARK 500 15 THR A 3 -40.64 -176.54 REMARK 500 15 SER A 4 -165.26 -179.72 REMARK 500 15 HIS A 11 -59.72 -137.64 REMARK 500 15 THR A 13 37.99 81.19 REMARK 500 15 HIS A 22 -110.80 -70.82 REMARK 500 15 CYS A 23 154.16 174.76 REMARK 500 15 MET A 25 -59.88 -132.13 REMARK 500 15 SER A 27 36.08 95.30 REMARK 500 16 THR A 3 110.68 60.57 REMARK 500 16 SER A 4 -71.02 -82.14 REMARK 500 16 HIS A 11 -59.29 -137.48 REMARK 500 16 THR A 13 37.90 81.07 REMARK 500 16 HIS A 22 -110.76 -71.62 REMARK 500 16 CYS A 23 153.18 174.60 REMARK 500 16 MET A 25 -59.94 -132.43 REMARK 500 16 SER A 27 35.86 95.51 REMARK 500 17 THR A 3 119.01 -163.61 REMARK 500 17 SER A 4 -170.97 -59.80 REMARK 500 17 HIS A 11 -59.86 -137.93 REMARK 500 17 THR A 13 38.42 80.85 REMARK 500 17 HIS A 22 -109.31 -70.71 REMARK 500 17 CYS A 23 151.40 173.90 REMARK 500 17 MET A 25 -61.11 -133.50 REMARK 500 17 SER A 27 35.71 97.08 REMARK 500 18 SER A 2 76.78 -164.68 REMARK 500 18 SER A 4 -75.03 -155.35 REMARK 500 18 HIS A 11 -58.32 -138.47 REMARK 500 18 THR A 13 36.63 83.01 REMARK 500 18 HIS A 22 -109.85 -70.83 REMARK 500 18 CYS A 23 158.26 173.92 REMARK 500 18 MET A 25 -61.66 -133.02 REMARK 500 18 SER A 27 36.12 96.50 REMARK 500 19 THR A 3 150.88 62.15 REMARK 500 19 SER A 4 -77.90 -73.68 REMARK 500 19 HIS A 11 -59.23 -137.86 REMARK 500 19 THR A 13 38.33 80.99 REMARK 500 19 HIS A 22 -108.81 -71.50 REMARK 500 19 CYS A 23 152.00 174.00 REMARK 500 19 MET A 25 -62.07 -133.39 REMARK 500 19 SER A 27 35.49 98.70 REMARK 500 20 SER A 2 -69.33 -90.16 REMARK 500 20 THR A 3 119.30 62.61 REMARK 500 20 SER A 4 -76.19 -60.05 REMARK 500 20 HIS A 11 -59.15 -137.68 REMARK 500 20 THR A 13 37.65 81.31 REMARK 500 20 HIS A 22 -111.07 -71.56 REMARK 500 20 CYS A 23 155.70 174.98 REMARK 500 20 MET A 25 -59.76 -132.30 REMARK 500 20 SER A 27 36.58 95.35 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 1 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.PDB RELATED DB: PDB REMARK 900 STRUCTURALLY RELATED TO REBREDOXIN REMARK 900 RELATED ID: 1DVB.PDB 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