HEADER TRANSCRIPTION 26-JAN-15 2RV1 TITLE SOLUTION STRUCTURES OF THE DNA-BINDING DOMAIN (ZF13) OF IMMUNE-RELATED TITLE 2 ZINC-FINGER PROTEIN ZFAT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER PROTEIN ZFAT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 878-907; COMPND 5 SYNONYM: ZINC FINGER GENE IN AITD SUSCEPTIBILITY REGION, ZINC FINGER COMPND 6 PROTEIN 406; COMPND 7 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: ZFAT, KIAA1485, ZFAT1, ZNF406; SOURCE 6 EXPRESSION_SYSTEM: CELL-FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: P060718-07 KEYWDS ZFAT, ZINC FINGER, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.TOCHIO,T.UMEHARA,T.KIGAWA,S.YOKOYAMA REVDAT 2 21-DEC-16 2RV1 1 JRNL REVDAT 1 08-APR-15 2RV1 0 JRNL AUTH N.TOCHIO,T.UMEHARA,K.NAKABAYASHI,M.YONEYAMA,K.TSUDA, JRNL AUTH 2 M.SHIROUZU,S.KOSHIBA,S.WATANABE,T.KIGAWA,T.SASAZUKI, JRNL AUTH 3 S.SHIRASAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURES OF THE DNA-BINDING DOMAINS OF JRNL TITL 2 IMMUNE-RELATED ZINC-FINGER PROTEIN ZFAT JRNL REF J.STRUCT.FUNCT.GENOM. V. 16 55 2015 JRNL REFN ISSN 1345-711X JRNL PMID 25801860 JRNL DOI 10.1007/S10969-015-9196-3 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RV1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-FEB-15. REMARK 100 THE RCSB ID CODE IS RCSB150300. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.12 MM [U-13C; U-15N] PROTEIN- REMARK 210 1, 20 MM [U-2H] TRIS-2, 100 MM REMARK 210 SODIUM CHLORIDE-3, 1 MM [U-2H] REMARK 210 DTT-4, 0.02 % SODIUM AZIDE-5, 50 REMARK 210 UM ZINC CHLORIDE-6, 90 % H2O-7, REMARK 210 10 % [U-2H] D2O-8, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C 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 : XWINNMR, NMRPIPE, NMRVIEW, REMARK 210 KUJIRA, CYANA, AMBER REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES 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: 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 3 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 15 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 20 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.3 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 2 ARG A 8 18.20 55.88 REMARK 500 3 LYS A 21 9.50 -65.81 REMARK 500 4 CYS A 15 -132.34 -125.69 REMARK 500 6 LYS A 21 171.27 57.24 REMARK 500 8 SER A 3 -57.31 -135.40 REMARK 500 8 LYS A 21 27.27 47.98 REMARK 500 10 ARG A 8 17.29 55.53 REMARK 500 11 MET A 20 26.67 -140.11 REMARK 500 12 LYS A 21 16.65 -63.34 REMARK 500 13 LYS A 21 40.19 -71.39 REMARK 500 14 ARG A 8 45.73 -77.24 REMARK 500 15 LYS A 21 -114.23 52.54 REMARK 500 16 LYS A 21 -40.37 57.73 REMARK 500 17 ASN A 22 117.97 51.18 REMARK 500 18 LYS A 21 -29.77 51.96 REMARK 500 20 LYS A 21 -179.46 55.33 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 10 ARG A 28 0.09 SIDE CHAIN 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 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 33 NE2 REMARK 620 2 HIS A 29 NE2 104.4 REMARK 620 3 CYS A 15 SG 109.5 112.1 REMARK 620 4 CYS A 12 SG 111.5 108.9 110.3 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 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ELP RELATED DB: PDB REMARK 900 RELATED ID: 11481 RELATED DB: BMRB REMARK 900 RELATED ID: 2RUT RELATED DB: PDB REMARK 900 RELATED ID: 2RUU RELATED DB: PDB REMARK 900 RELATED ID: 2RUV RELATED DB: PDB REMARK 900 RELATED ID: 2RUW RELATED DB: PDB REMARK 900 RELATED ID: 2RUX RELATED DB: PDB REMARK 900 RELATED ID: 2RUY RELATED DB: PDB REMARK 900 RELATED ID: 2RUZ RELATED DB: PDB REMARK 900 RELATED ID: 2RV0 RELATED DB: PDB REMARK 900 RELATED ID: 2RV2 RELATED DB: PDB REMARK 900 RELATED ID: 2RV3 RELATED DB: PDB REMARK 900 RELATED ID: 2RV4 RELATED DB: PDB REMARK 900 RELATED ID: 2RV5 RELATED DB: PDB REMARK 900 RELATED ID: 2RV6 RELATED DB: PDB REMARK 900 RELATED ID: 2RV7 RELATED DB: PDB DBREF 2RV1 A 8 37 UNP Q9P243 ZFAT_HUMAN 878 907 SEQADV 2RV1 GLY A 1 UNP Q9P243 EXPRESSION TAG SEQADV 2RV1 SER A 2 UNP Q9P243 EXPRESSION TAG SEQADV 2RV1 SER A 3 UNP Q9P243 EXPRESSION TAG SEQADV 2RV1 GLY A 4 UNP Q9P243 EXPRESSION TAG SEQADV 2RV1 SER A 5 UNP Q9P243 EXPRESSION TAG SEQADV 2RV1 SER A 6 UNP Q9P243 EXPRESSION TAG SEQADV 2RV1 GLY A 7 UNP Q9P243 EXPRESSION TAG SEQRES 1 A 37 GLY SER SER GLY SER SER GLY ARG ALA MET LYS CYS PRO SEQRES 2 A 37 TYR CYS ASP PHE TYR PHE MET LYS ASN GLY SER ASP LEU SEQRES 3 A 37 GLN ARG HIS ILE TRP ALA HIS GLU GLY VAL LYS HET ZN A 101 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 SER A 24 GLU A 34 1 11 SHEET 1 A 2 MET A 10 LYS A 11 0 SHEET 2 A 2 TYR A 18 PHE A 19 -1 O PHE A 19 N MET A 10 LINK NE2 HIS A 33 ZN ZN A 101 1555 1555 1.91 LINK NE2 HIS A 29 ZN ZN A 101 1555 1555 1.91 LINK SG CYS A 15 ZN ZN A 101 1555 1555 2.17 LINK SG CYS A 12 ZN ZN A 101 1555 1555 2.17 SITE 1 AC1 4 CYS A 12 CYS A 15 HIS A 29 HIS A 33 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