PDB Short entry for 2EJ4 HEADER GENE REGULATION 14-MAR-07 2EJ4 TITLE FUNCTIONAL AND STRUCTURAL BASIS OF NUCLEAR LOCALIZATION SIGNAL IN ZIC3 TITLE 2 ZINC FINGER DOMAIN: A ROLE OF CONSERVED TRYPTOPHAN RESIDUE IN THE TITLE 3 ZINC FINGER DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER PROTEIN ZIC 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZIC3_C2H2-12 DOMAIN, UNP RESIDUES 245-326; COMPND 5 SYNONYM: ZINC FINGER PROTEIN OF THE CEREBELLUM 3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ZIC3; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050815-02; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS ZF-C2H2 DOMAIN, ZINC BINDING, STRUCTURAL GENOMICS, NPPSFA, NATIONAL KEYWDS 2 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2EJ4 1 REMARK SEQADV REVDAT 2 24-FEB-09 2EJ4 1 VERSN REVDAT 1 05-FEB-08 2EJ4 0 JRNL AUTH M.HATAYAMA,T.TOMIZAWA,P.BOUVAGNET,S.YOKOYAMA,K.MIKOSHIBA, JRNL AUTH 2 T.KIGAWA,J.ARUGA JRNL TITL FUNCTIONAL AND STRUCTURAL BASIS OF NUCLEAR LOCALIZATION JRNL TITL 2 SIGNAL IN ZIC3 ZINC FINGER DOMAIN: A ROLE OF CONSERVED JRNL TITL 3 TRYPTOPHAN RESIDUE IN THE ZINC FINGER DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, CYANA 2.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2EJ4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000026726. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.13MM ZIC3_C2H2-12 U-15N,13C; REMARK 210 20MM D-MALONIC ACID-NAOH(PH6.0); REMARK 210 100MM NACL; 0.1MM D-DTT; 0.02% REMARK 210 NAN3; 0.05MM ZNCL2; 1MM NTA; 90% REMARK 210 H2O,10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.932, CYANA 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINTED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: 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 ILE A 10 160.19 -42.58 REMARK 500 1 SER A 15 158.36 61.37 REMARK 500 1 ASP A 20 178.64 -54.70 REMARK 500 1 ALA A 22 -0.54 71.34 REMARK 500 1 GLN A 23 142.11 -35.67 REMARK 500 1 LYS A 28 93.05 -38.50 REMARK 500 1 ASP A 32 116.96 82.90 REMARK 500 1 HIS A 49 -80.20 -110.83 REMARK 500 1 ASN A 57 113.09 77.80 REMARK 500 1 GLU A 68 32.89 34.73 REMARK 500 1 LYS A 70 107.81 -34.72 REMARK 500 1 SER A 71 -157.52 -71.91 REMARK 500 1 GLU A 88 -157.21 -80.07 REMARK 500 1 SER A 93 78.44 39.15 REMARK 500 2 ILE A 10 157.22 -45.74 REMARK 500 2 ASP A 20 -156.93 -60.15 REMARK 500 2 GLU A 21 -54.73 -143.86 REMARK 500 2 LYS A 28 99.21 -41.24 REMARK 500 2 ASP A 32 152.40 61.15 REMARK 500 2 ARG A 33 173.93 173.69 REMARK 500 2 HIS A 49 -80.28 -112.39 REMARK 500 2 ASN A 57 96.58 80.80 REMARK 500 2 GLU A 68 26.35 39.42 REMARK 500 2 SER A 71 155.72 81.64 REMARK 500 2 LYS A 73 -39.50 82.54 REMARK 500 2 GLU A 88 -154.58 -81.03 REMARK 500 2 SER A 90 45.25 -81.89 REMARK 500 3 ILE A 10 155.02 -47.10 REMARK 500 3 LYS A 11 -166.90 -112.55 REMARK 500 3 GLN A 12 170.86 -58.02 REMARK 500 3 SER A 15 129.15 65.01 REMARK 500 3 ASP A 20 177.85 -57.30 REMARK 500 3 GLN A 23 142.48 -36.95 REMARK 500 3 LYS A 28 95.93 -37.02 REMARK 500 3 ASP A 32 -90.56 54.86 REMARK 500 3 ARG A 33 175.67 54.46 REMARK 500 3 HIS A 49 -78.59 -113.31 REMARK 500 3 ASN A 57 92.20 82.38 REMARK 500 3 LYS A 77 -19.03 -49.07 REMARK 500 3 GLU A 88 -155.79 -92.42 REMARK 500 3 SER A 90 144.92 -172.84 REMARK 500 3 SER A 93 -169.84 -68.45 REMARK 500 3 SER A 94 -160.03 -62.88 REMARK 500 4 SER A 5 20.33 -150.38 REMARK 500 4 SER A 6 -39.81 -38.81 REMARK 500 4 ILE A 10 164.39 -44.46 REMARK 500 4 GLN A 12 175.98 -52.23 REMARK 500 4 SER A 15 155.64 76.98 REMARK 500 4 ASP A 20 -177.74 -62.96 REMARK 500 4 LYS A 28 93.05 -42.86 REMARK 500 REMARK 500 THIS ENTRY HAS 303 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 16 SG REMARK 620 2 CYS A 31 SG 102.0 REMARK 620 3 HIS A 44 NE2 117.2 114.4 REMARK 620 4 HIS A 49 NE2 103.7 99.1 117.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 60 SG REMARK 620 2 CYS A 65 SG 115.3 REMARK 620 3 HIS A 81 NE2 117.1 115.5 REMARK 620 4 HIS A 85 NE2 99.8 107.0 98.5 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: AR_001000441.1 RELATED DB: TARGETDB DBREF 2EJ4 A 8 89 UNP O60481 ZIC3_HUMAN 245 326 SEQADV 2EJ4 GLY A 1 UNP O60481 EXPRESSION TAG SEQADV 2EJ4 SER A 2 UNP O60481 EXPRESSION TAG SEQADV 2EJ4 SER A 3 UNP O60481 EXPRESSION TAG SEQADV 2EJ4 GLY A 4 UNP O60481 EXPRESSION TAG SEQADV 2EJ4 SER A 5 UNP O60481 EXPRESSION TAG SEQADV 2EJ4 SER A 6 UNP O60481 EXPRESSION TAG SEQADV 2EJ4 GLY A 7 UNP O60481 EXPRESSION TAG SEQADV 2EJ4 SER A 90 UNP O60481 EXPRESSION TAG SEQADV 2EJ4 GLY A 91 UNP O60481 EXPRESSION TAG SEQADV 2EJ4 PRO A 92 UNP O60481 EXPRESSION TAG SEQADV 2EJ4 SER A 93 UNP O60481 EXPRESSION TAG SEQADV 2EJ4 SER A 94 UNP O60481 EXPRESSION TAG SEQADV 2EJ4 GLY A 95 UNP O60481 EXPRESSION TAG SEQRES 1 A 95 GLY SER SER GLY SER SER GLY GLN PRO ILE LYS GLN GLU SEQRES 2 A 95 LEU SER CYS LYS TRP ILE ASP GLU ALA GLN LEU SER ARG SEQRES 3 A 95 PRO LYS LYS SER CYS ASP ARG THR PHE SER THR MET HIS SEQRES 4 A 95 GLU LEU VAL THR HIS VAL THR MET GLU HIS VAL GLY GLY SEQRES 5 A 95 PRO GLU GLN ASN ASN HIS VAL CYS TYR TRP GLU GLU CYS SEQRES 6 A 95 PRO ARG GLU GLY LYS SER PHE LYS ALA LYS TYR LYS LEU SEQRES 7 A 95 VAL ASN HIS ILE ARG VAL HIS THR GLY GLU LYS SER GLY SEQRES 8 A 95 PRO SER SER GLY HET ZN A 201 1 HET ZN A 401 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 THR A 37 GLU A 48 1 12 HELIX 2 2 ALA A 74 GLY A 87 1 14 LINK SG CYS A 16 ZN ZN A 201 1555 1555 2.22 LINK SG CYS A 31 ZN ZN A 201 1555 1555 2.37 LINK NE2 HIS A 44 ZN ZN A 201 1555 1555 2.03 LINK NE2 HIS A 49 ZN ZN A 201 1555 1555 2.00 LINK SG CYS A 60 ZN ZN A 401 1555 1555 2.29 LINK SG CYS A 65 ZN ZN A 401 1555 1555 2.39 LINK NE2 HIS A 81 ZN ZN A 401 1555 1555 1.97 LINK NE2 HIS A 85 ZN ZN A 401 1555 1555 2.06 CISPEP 1 ARG A 26 PRO A 27 1 0.00 CISPEP 2 ARG A 26 PRO A 27 2 -0.09 CISPEP 3 ARG A 26 PRO A 27 3 -0.01 CISPEP 4 ARG A 26 PRO A 27 4 0.00 CISPEP 5 ARG A 26 PRO A 27 5 0.09 CISPEP 6 ARG A 26 PRO A 27 6 0.00 CISPEP 7 ARG A 26 PRO A 27 7 0.03 CISPEP 8 ARG A 26 PRO A 27 8 0.00 CISPEP 9 ARG A 26 PRO A 27 9 0.05 CISPEP 10 ARG A 26 PRO A 27 10 0.00 CISPEP 11 ARG A 26 PRO A 27 11 -0.01 CISPEP 12 ARG A 26 PRO A 27 12 0.00 CISPEP 13 ARG A 26 PRO A 27 13 0.01 CISPEP 14 ARG A 26 PRO A 27 14 -0.01 CISPEP 15 ARG A 26 PRO A 27 15 -0.09 CISPEP 16 ARG A 26 PRO A 27 16 0.02 CISPEP 17 ARG A 26 PRO A 27 17 -0.01 CISPEP 18 ARG A 26 PRO A 27 18 0.00 CISPEP 19 ARG A 26 PRO A 27 19 0.03 CISPEP 20 ARG A 26 PRO A 27 20 -0.01 SITE 1 AC1 4 CYS A 16 CYS A 31 HIS A 44 HIS A 49 SITE 1 AC2 4 CYS A 60 CYS A 65 HIS A 81 HIS A 85 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