PDB Short entry for 2YT9 HEADER TRANSCRIPTION 05-APR-07 2YT9 TITLE SOLUTION STRUCTURE OF C2H2 TYPE ZINC FINGER DOMAIN 345 IN ZINC FINGER TITLE 2 PROTEIN 278 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C2H2 DOMAIN; COMPND 5 SYNONYM: ZINC FINGER PROTEIN 278, ZINC FINGER SARCOMA GENE PROTEIN, COMPND 6 BTB-POZ DOMAIN ZINC FINGER TRANSCRIPTION FACTOR, PROTEIN KINASE A RI- COMPND 7 SUBUNIT ALPHA- ASSOCIATED PROTEIN, ZINC FINGER AND BTB DOMAIN- COMPND 8 CONTAINING PROTEIN 19; COMPND 9 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: PATZ, RIAZ, ZBTB19, ZNF278, ZSG; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P060718-20; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS ZINC-FINGER, C2H2, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON KEYWDS 2 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.KASAHARA,K.TSUDA,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA,M.SHIROUZU, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 16-MAR-22 2YT9 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2YT9 1 VERSN REVDAT 1 09-OCT-07 2YT9 0 JRNL AUTH N.KASAHARA,K.TSUDA,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA, JRNL AUTH 2 M.SHIROUZU,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF C2H2 TYPE ZINC FINGER DOMAIN 345 IN JRNL TITL 2 ZINC FINGER PROTEIN 278 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 2.0.17 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUTERT,P (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YT9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000027105. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20MM D-TRIS-HCL (PH7.0), 100MM REMARK 210 NACL, 1MM D-DTT, 0.02% NAN3, REMARK 210 0.05MM ZNCL2+1MM IDA, 90% H2O,10% REMARK 210 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 20060702, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9820, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE REMARK 210 DYNAMICS,RESTRAINTED MOLECULAR REMARK 210 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 366 -43.41 -131.72 REMARK 500 1 GLU A 387 85.94 54.22 REMARK 500 1 VAL A 394 -66.28 -93.27 REMARK 500 1 ASP A 413 77.15 60.89 REMARK 500 1 SER A 424 -75.69 -109.27 REMARK 500 1 LYS A 427 -75.98 -85.94 REMARK 500 1 SER A 444 92.90 63.37 REMARK 500 2 SER A 360 60.06 -112.96 REMARK 500 2 ILE A 366 -43.57 -134.16 REMARK 500 2 SER A 385 149.68 -177.08 REMARK 500 2 GLU A 387 50.12 -170.50 REMARK 500 2 SER A 415 109.62 -177.04 REMARK 500 2 SER A 424 -75.81 -109.98 REMARK 500 2 LYS A 427 -76.10 -84.21 REMARK 500 2 SER A 444 70.93 51.94 REMARK 500 2 PRO A 446 95.09 -69.77 REMARK 500 3 SER A 357 106.16 -176.70 REMARK 500 3 ILE A 366 -41.37 -132.54 REMARK 500 3 VAL A 394 -64.49 -91.63 REMARK 500 3 ASP A 413 175.96 63.28 REMARK 500 3 SER A 424 -75.70 -109.66 REMARK 500 3 LYS A 427 -76.12 -84.38 REMARK 500 4 ILE A 366 -40.09 -131.40 REMARK 500 4 SER A 424 -75.80 -109.98 REMARK 500 4 LYS A 427 -76.48 -89.31 REMARK 500 4 SER A 444 178.18 58.19 REMARK 500 4 SER A 447 113.62 -164.20 REMARK 500 5 SER A 357 88.99 55.79 REMARK 500 5 SER A 359 -179.01 57.08 REMARK 500 5 SER A 360 -173.39 62.83 REMARK 500 5 GLU A 365 30.58 -96.09 REMARK 500 5 ILE A 366 -39.83 -131.14 REMARK 500 5 HIS A 384 -74.53 -51.93 REMARK 500 5 VAL A 394 -66.69 -93.08 REMARK 500 5 LEU A 397 172.23 -54.14 REMARK 500 5 SER A 424 -75.65 -109.95 REMARK 500 5 LYS A 427 -76.30 -89.06 REMARK 500 5 HIS A 443 45.96 -91.45 REMARK 500 6 GLU A 387 -169.64 -68.89 REMARK 500 6 SER A 424 -75.75 -109.85 REMARK 500 6 LYS A 427 -76.05 -82.24 REMARK 500 6 GLN A 441 -66.86 -93.71 REMARK 500 7 SER A 357 -171.93 -61.32 REMARK 500 7 GLU A 387 74.20 57.62 REMARK 500 7 ARG A 404 -61.48 -91.01 REMARK 500 7 SER A 424 -75.62 -109.37 REMARK 500 7 LYS A 427 -76.00 -85.07 REMARK 500 7 GLN A 441 -66.77 -102.03 REMARK 500 7 VAL A 442 -70.92 -59.20 REMARK 500 7 SER A 447 -72.86 -96.94 REMARK 500 REMARK 500 THIS ENTRY HAS 156 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 364 SG REMARK 620 2 CYS A 367 SG 107.1 REMARK 620 3 HIS A 380 NE2 111.8 109.1 REMARK 620 4 HIS A 384 NE2 115.6 116.5 96.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 392 SG REMARK 620 2 CYS A 395 SG 114.1 REMARK 620 3 HIS A 408 NE2 110.3 104.6 REMARK 620 4 HIS A 412 NE2 116.7 105.2 104.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 422 SG REMARK 620 2 CYS A 425 SG 112.9 REMARK 620 3 HIS A 438 NE2 110.4 96.8 REMARK 620 4 HIS A 443 NE2 106.6 120.7 108.9 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 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSI002013231.5 RELATED DB: TARGETDB DBREF 2YT9 A 362 443 UNP Q9HBE1 PATZ1_HUMAN 355 436 SEQADV 2YT9 GLY A 355 UNP Q9HBE1 EXPRESSION TAG SEQADV 2YT9 SER A 356 UNP Q9HBE1 EXPRESSION TAG SEQADV 2YT9 SER A 357 UNP Q9HBE1 EXPRESSION TAG SEQADV 2YT9 GLY A 358 UNP Q9HBE1 EXPRESSION TAG SEQADV 2YT9 SER A 359 UNP Q9HBE1 EXPRESSION TAG SEQADV 2YT9 SER A 360 UNP Q9HBE1 EXPRESSION TAG SEQADV 2YT9 GLY A 361 UNP Q9HBE1 EXPRESSION TAG SEQADV 2YT9 SER A 444 UNP Q9HBE1 EXPRESSION TAG SEQADV 2YT9 GLY A 445 UNP Q9HBE1 EXPRESSION TAG SEQADV 2YT9 PRO A 446 UNP Q9HBE1 EXPRESSION TAG SEQADV 2YT9 SER A 447 UNP Q9HBE1 EXPRESSION TAG SEQADV 2YT9 SER A 448 UNP Q9HBE1 EXPRESSION TAG SEQADV 2YT9 GLY A 449 UNP Q9HBE1 EXPRESSION TAG SEQRES 1 A 95 GLY SER SER GLY SER SER GLY VAL ALA CYS GLU ILE CYS SEQRES 2 A 95 GLY LYS ILE PHE ARG ASP VAL TYR HIS LEU ASN ARG HIS SEQRES 3 A 95 LYS LEU SER HIS SER GLY GLU LYS PRO TYR SER CYS PRO SEQRES 4 A 95 VAL CYS GLY LEU ARG PHE LYS ARG LYS ASP ARG MET SER SEQRES 5 A 95 TYR HIS VAL ARG SER HIS ASP GLY SER VAL GLY LYS PRO SEQRES 6 A 95 TYR ILE CYS GLN SER CYS GLY LYS GLY PHE SER ARG PRO SEQRES 7 A 95 ASP HIS LEU ASN GLY HIS ILE LYS GLN VAL HIS SER GLY SEQRES 8 A 95 PRO SER SER GLY HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HETNAM ZN ZINC ION FORMUL 2 ZN 3(ZN 2+) HELIX 1 1 VAL A 374 HIS A 384 1 11 HELIX 2 2 ARG A 401 ASP A 413 1 13 HELIX 3 3 ARG A 431 VAL A 442 1 12 SHEET 1 A 2 VAL A 362 ALA A 363 0 SHEET 2 A 2 ILE A 370 PHE A 371 -1 O PHE A 371 N VAL A 362 SHEET 1 B 2 TYR A 390 SER A 391 0 SHEET 2 B 2 ARG A 398 PHE A 399 -1 O PHE A 399 N TYR A 390 LINK ZN ZN A 201 SG CYS A 364 1555 1555 2.36 LINK ZN ZN A 201 SG CYS A 367 1555 1555 2.19 LINK ZN ZN A 201 NE2 HIS A 380 1555 1555 2.06 LINK ZN ZN A 201 NE2 HIS A 384 1555 1555 2.00 LINK ZN ZN A 202 SG CYS A 392 1555 1555 2.37 LINK ZN ZN A 202 SG CYS A 395 1555 1555 2.36 LINK ZN ZN A 202 NE2 HIS A 408 1555 1555 1.89 LINK ZN ZN A 202 NE2 HIS A 412 1555 1555 1.89 LINK ZN ZN A 203 SG CYS A 422 1555 1555 2.41 LINK ZN ZN A 203 SG CYS A 425 1555 1555 2.33 LINK ZN ZN A 203 NE2 HIS A 438 1555 1555 2.10 LINK ZN ZN A 203 NE2 HIS A 443 1555 1555 1.95 CISPEP 1 LYS A 388 PRO A 389 1 -0.07 CISPEP 2 LYS A 388 PRO A 389 2 -0.16 CISPEP 3 LYS A 388 PRO A 389 3 -0.08 CISPEP 4 LYS A 388 PRO A 389 4 -0.10 CISPEP 5 LYS A 388 PRO A 389 5 -0.08 CISPEP 6 LYS A 388 PRO A 389 6 -0.23 CISPEP 7 LYS A 388 PRO A 389 7 -0.04 CISPEP 8 LYS A 388 PRO A 389 8 -0.18 CISPEP 9 LYS A 388 PRO A 389 9 -0.12 CISPEP 10 LYS A 388 PRO A 389 10 -0.10 CISPEP 11 LYS A 388 PRO A 389 11 -0.08 CISPEP 12 LYS A 388 PRO A 389 12 -0.12 CISPEP 13 LYS A 388 PRO A 389 13 -0.10 CISPEP 14 LYS A 388 PRO A 389 14 -0.11 CISPEP 15 LYS A 388 PRO A 389 15 -0.14 CISPEP 16 LYS A 388 PRO A 389 16 -0.11 CISPEP 17 LYS A 388 PRO A 389 17 -0.12 CISPEP 18 LYS A 388 PRO A 389 18 -0.09 CISPEP 19 LYS A 388 PRO A 389 19 -0.11 CISPEP 20 LYS A 388 PRO A 389 20 -0.02 SITE 1 AC1 4 CYS A 364 CYS A 367 HIS A 380 HIS A 384 SITE 1 AC2 4 CYS A 392 CYS A 395 HIS A 408 HIS A 412 SITE 1 AC3 4 CYS A 422 CYS A 425 HIS A 438 HIS A 443 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