HEADER PROTEIN BINDING 11-AUG-03 1Q5W TITLE UBIQUITIN RECOGNITION BY NPL4 ZINC-FINGERS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMOLOG OF YEAST NUCLEAR PROTEIN LOCALIZATION 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NPL4 NZF DOMAIN (RESIDUES 580-608); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UBIQUITIN; COMPND 8 CHAIN: B; COMPND 9 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: T7; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX2T; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: (UBA52 OR UBCEP2) AND UBB AND UBC AND (UBA80 OR UBCEP1 OR SOURCE 16 RPS27A); SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: T7; SOURCE 21 EXPRESSION_SYSTEM_PLASMID: PET3D KEYWDS UBIQUITIN, PROTEIN-PROTEIN COMPLEX, ZINC-FINGER, RUBREDOXIN KNUCKLE, KEYWDS 2 NZF DOMAIN, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.L.ALAM,J.SUN,M.PAYNE,B.D.WELCH,B.K.BLAKE,D.R.DAVIS,H.H.MEYER, AUTHOR 2 S.D.EMR,W.I.SUNDQUIST REVDAT 4 02-MAR-22 1Q5W 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1Q5W 1 VERSN REVDAT 2 13-APR-04 1Q5W 1 JRNL REVDAT 1 30-MAR-04 1Q5W 0 JRNL AUTH S.L.ALAM,J.SUN,M.PAYNE,B.D.WELCH,B.K.BLAKE,D.R.DAVIS, JRNL AUTH 2 H.H.MEYER,S.D.EMR,W.I.SUNDQUIST JRNL TITL UBIQUITIN INTERACTIONS OF NZF ZINC FINGERS. JRNL REF EMBO J. V. 23 1411 2004 JRNL REFN ISSN 0261-4189 JRNL PMID 15029239 JRNL DOI 10.1038/SJ.EMBOJ.7600114 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.WANG,S.L.ALAM,H.H.MEYER,M.PAYNE,T.L.STEMMLER,D.R.DAVIS, REMARK 1 AUTH 2 W.I.SUNDQUIST REMARK 1 TITL STRUCTURE AND UBIQUITIN INTERACTIONS OF THE CONSERVED ZINC REMARK 1 TITL 2 FINGER DOMAIN OF NPL4. REMARK 1 REF J.BIOL.CHEM. V. 278 20225 2003 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M300459200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, CNS 1.1 REMARK 3 AUTHORS : PETER GUNTERT (DYANA), "CRYSTALLOGRAPHY AND NMR REMARK 3 SYSTEM (CNS): A NEW SOFTWARE SYSTEM (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURES ARE BASED ON 2072 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 145 DIHEDRAL ANGLE CONSTRAINTS ,104 H-BOND REMARK 3 CONSTRAINTS, AND 14 ZINC-COORDINATION CONSTRAINTS. REMARK 4 REMARK 4 1Q5W COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-03. REMARK 100 THE DEPOSITION ID IS D_1000019955. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 291; 291; 291; 291 REMARK 210 PH : 5.5; 5.5; 5.5; 5.5 REMARK 210 IONIC STRENGTH : 70MM; 70MM; 70MM; 70MM REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM NPL4 NZF U-15N,13C; 2MM REMARK 210 UNLABELED-UBIQUITIN; 20MM REMARK 210 PHOSPHATE BUFFER PH 5.5, 50MM REMARK 210 NACL; 90% H2O, 10%; 1MM REMARK 210 UBIQUITIN U-15N,13C; 2MM REMARK 210 UNLABELED-NPL4 NZF; 20MM REMARK 210 PHOSPHATE BUFFER PH 5.5, 50MM REMARK 210 NACL; 90% H2O, 10%; 1MM REMARK 210 UBIQUITIN U-15N; 2MM UNLABELED- REMARK 210 NPL4 NZF; 20MM PHOSPHATE BUFFER REMARK 210 PH 5.5, 50MM; 1MM NPL4 NZF U-15N; REMARK 210 2MM UNLABELED-UBIQUITIN; 20MM REMARK 210 PHOSPHATE BUFFER PH 5.5, 50MM REMARK 210 NACL; 90% H2O, 10% REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNCACB, REMARK 210 CBCACONH, CCONH, HCCONH,HNCO, REMARK 210 HNCACO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA 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 FOLLOWED REMARK 210 BY SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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,TARGET REMARK 210 FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: INTER-MOLECULAR NOES IDENTIFIED WITH HALF-FILTERED AND REMARK 210 DOUBLE HALF-FILTERED NOE EXPERIMENTS AND SAMPLES #1 AND #2. 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 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 SER A 4 -170.19 -65.56 REMARK 500 1 CYS A 9 157.59 -46.57 REMARK 500 1 HIS A 11 -57.86 -131.99 REMARK 500 1 THR A 13 23.53 81.06 REMARK 500 1 ASP B 121 -167.62 -63.98 REMARK 500 1 ASN B 160 44.04 86.63 REMARK 500 2 SER A 2 144.16 -176.64 REMARK 500 2 THR A 3 31.60 -98.90 REMARK 500 2 ALA A 5 122.90 -177.63 REMARK 500 2 CYS A 9 157.21 -47.57 REMARK 500 2 HIS A 11 -57.81 -132.31 REMARK 500 2 ASP B 121 -165.12 -61.92 REMARK 500 2 ASN B 160 51.46 85.74 REMARK 500 2 SER B 165 173.30 -59.00 REMARK 500 2 ARG B 174 -169.16 46.24 REMARK 500 3 THR A 3 102.41 -176.71 REMARK 500 3 ALA A 5 -176.23 62.07 REMARK 500 3 CYS A 9 157.45 -46.79 REMARK 500 3 HIS A 11 -54.11 -137.81 REMARK 500 3 THR A 13 74.19 54.77 REMARK 500 3 ASP B 121 -168.07 -65.29 REMARK 500 3 ALA B 146 41.69 39.13 REMARK 500 3 ASN B 160 50.47 83.89 REMARK 500 4 SER A 2 -40.43 -176.42 REMARK 500 4 ALA A 5 50.85 -92.62 REMARK 500 4 CYS A 9 157.41 -48.64 REMARK 500 4 HIS A 11 -57.37 -130.73 REMARK 500 4 MET A 25 -58.92 -123.02 REMARK 500 4 ASP B 121 -167.66 -64.37 REMARK 500 4 ASN B 160 49.72 84.29 REMARK 500 5 SER A 2 102.56 60.83 REMARK 500 5 SER A 4 -74.81 -127.99 REMARK 500 5 ALA A 5 50.30 -166.36 REMARK 500 5 CYS A 9 157.45 -47.78 REMARK 500 5 HIS A 11 -55.89 -135.25 REMARK 500 5 MET A 25 -59.65 -123.04 REMARK 500 5 ASP B 121 -165.60 -58.09 REMARK 500 5 ASN B 160 50.62 86.59 REMARK 500 5 SER B 165 171.96 -58.58 REMARK 500 6 SER A 2 106.58 -161.90 REMARK 500 6 THR A 3 155.62 60.36 REMARK 500 6 CYS A 9 157.19 -47.22 REMARK 500 6 HIS A 11 -56.80 -137.53 REMARK 500 6 ASP B 121 -165.28 -60.31 REMARK 500 6 ASN B 160 50.17 86.77 REMARK 500 7 SER A 2 113.79 61.62 REMARK 500 7 THR A 3 -69.36 -163.75 REMARK 500 7 ALA A 5 124.54 -176.82 REMARK 500 7 CYS A 9 157.41 -46.40 REMARK 500 7 HIS A 11 -54.36 -130.21 REMARK 500 REMARK 500 THIS ENTRY HAS 154 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 9 SG REMARK 620 2 CYS A 12 SG 107.4 REMARK 620 3 CYS A 23 SG 104.2 113.0 REMARK 620 4 CYS A 26 SG 103.7 124.8 101.7 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: 1NJ3 RELATED DB: PDB REMARK 900 NPL4 ZINC FINGER STRUCTURE DBREF 1Q5W A 3 31 UNP Q9ES54 NPL4_RAT 580 608 DBREF 1Q5W B 101 176 UNP P62988 UBIQ_HUMAN 1 76 SEQADV 1Q5W GLY A 1 UNP Q9ES54 CLONING ARTIFACT SEQADV 1Q5W 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 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 HET ZN A 32 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ HELIX 1 1 THR B 122 GLU B 134 1 13 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 SHEET 1 B 4 THR B 112 GLU B 116 0 SHEET 2 B 4 GLN B 102 THR B 107 -1 N VAL B 105 O ILE B 113 SHEET 3 B 4 SER B 165 LEU B 171 1 O LEU B 167 N PHE B 104 SHEET 4 B 4 GLN B 141 ILE B 144 -1 N ILE B 144 O HIS B 168 LINK SG CYS A 9 ZN ZN A 32 1555 1555 2.38 LINK SG CYS A 12 ZN ZN A 32 1555 1555 2.32 LINK SG CYS A 23 ZN ZN A 32 1555 1555 2.41 LINK SG CYS A 26 ZN ZN A 32 1555 1555 2.38 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