HEADER TRANSCRIPTION/DNA 04-NOV-08 2KAE TITLE DATA-DRIVEN MODEL OF MED1:DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: GATA-TYPE TRANSCRIPTION FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 111-166; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*DCP*DGP*DGP*DAP*DAP*DAP*DAP*DGP*DTP*DAP*DTP*DAP*DCP*D COMPND 8 TP*DTP*DTP*DTP*DCP*DCP*DG)-3'; COMPND 9 CHAIN: C, B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: NEMATODE; SOURCE 4 ORGANISM_TAXID: 6239; SOURCE 5 GENE: MED-1, T24D3.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES KEYWDS ZINC FINGER, GATA-TYPE, DNA, TRANSCRIPTION FACTOR, METAL-BINDING, KEYWDS 2 ZINC, ZINC-FINGER, TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.A.LOWRY,R.GAMSJAEGER,S.THONG,W.HUNG,A.H.KWAN,G.BROITMAN-MADURO, AUTHOR 2 J.M.MATTHEWS,M.MADURO,J.P.MACKAY REVDAT 3 16-MAR-22 2KAE 1 REMARK DBREF SEQADV REVDAT 2 10-MAR-09 2KAE 1 JRNL REVDAT 1 06-JAN-09 2KAE 0 JRNL AUTH J.A.LOWRY,R.GAMSJAEGER,S.Y.THONG,W.HUNG,A.H.KWAN, JRNL AUTH 2 G.BROITMAN-MADURO,J.M.MATTHEWS,M.MADURO,J.P.MACKAY JRNL TITL STRUCTURAL ANALYSIS OF MED-1 REVEALS UNEXPECTED DIVERSITY IN JRNL TITL 2 THE MECHANISM OF DNA RECOGNITION BY GATA-TYPE ZINC FINGER JRNL TITL 3 DOMAINS. JRNL REF J.BIOL.CHEM. V. 284 5827 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19095651 JRNL DOI 10.1074/JBC.M808712200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HADDOCK REMARK 4 REMARK 4 2KAE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000100877. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 40 MM SODIUM CHLORIDE, 20 MM REMARK 210 POTASSIUM PHOSPHATE, 1 MM DTT, REMARK 210 90% H2O/10% D2O; 40 MM SODIUM REMARK 210 CHLORIDE, 20 MM POTASSIUM REMARK 210 PHOSPHATE, 1 MM DTT, 6 MG/ML PF1 REMARK 210 PHAGE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HNHA; 3D 1H-15N NOESY; 2D 1H-1H REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : 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 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 104 REMARK 465 SER A 105 REMARK 465 HIS A 106 REMARK 465 MET A 107 REMARK 465 ASN A 108 REMARK 465 LYS A 109 REMARK 465 LYS A 110 REMARK 465 GLU A 167 REMARK 465 THR A 168 REMARK 465 ASN A 169 REMARK 465 GLY A 170 REMARK 465 VAL A 171 REMARK 465 ASP A 172 REMARK 465 SER A 173 REMARK 465 PHE A 174 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 H22 DG C 28 O2 DC B 13 1.58 REMARK 500 H22 DG C 22 O2 DC B 19 1.59 REMARK 500 H62 DA C 24 O4 DT B 17 1.59 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 PHE A 112 -106.30 -127.43 REMARK 500 1 GLN A 113 157.70 174.29 REMARK 500 1 ASN A 116 -41.39 -159.86 REMARK 500 1 CYS A 117 -73.40 -90.59 REMARK 500 1 SER A 118 82.61 82.65 REMARK 500 1 ARG A 126 17.37 -165.71 REMARK 500 1 ILE A 128 83.80 45.98 REMARK 500 1 ARG A 129 96.09 -34.72 REMARK 500 1 SER A 130 -78.53 -153.33 REMARK 500 1 LYS A 131 -66.63 -144.54 REMARK 500 1 LYS A 148 -163.90 -162.67 REMARK 500 2 PHE A 112 -96.76 -105.81 REMARK 500 2 GLN A 113 160.57 165.59 REMARK 500 2 ASN A 116 -42.44 -160.00 REMARK 500 2 CYS A 117 -76.96 -92.88 REMARK 500 2 SER A 118 84.30 90.40 REMARK 500 2 ARG A 124 108.25 -173.70 REMARK 500 2 ARG A 126 22.04 -168.96 REMARK 500 2 ILE A 128 75.35 38.75 REMARK 500 2 ARG A 129 92.16 -31.98 REMARK 500 2 SER A 130 -73.42 -130.99 REMARK 500 2 LYS A 131 -64.56 -131.66 REMARK 500 2 GLU A 132 -157.74 -92.50 REMARK 500 2 ASN A 147 -37.79 -145.02 REMARK 500 2 LEU A 163 7.49 -69.15 REMARK 500 3 PHE A 112 -95.56 -94.96 REMARK 500 3 GLN A 113 163.30 167.89 REMARK 500 3 ASN A 116 -49.36 -163.27 REMARK 500 3 CYS A 117 -80.42 -88.09 REMARK 500 3 SER A 118 78.98 93.98 REMARK 500 3 ILE A 123 -8.59 -57.99 REMARK 500 3 ARG A 124 107.31 177.84 REMARK 500 3 ARG A 126 17.39 -167.74 REMARK 500 3 ILE A 128 80.16 47.66 REMARK 500 3 ARG A 129 95.75 -27.36 REMARK 500 3 SER A 130 -77.59 -151.11 REMARK 500 3 LYS A 131 -71.07 -127.99 REMARK 500 3 ASN A 147 -37.74 -132.65 REMARK 500 3 LEU A 163 8.59 -53.81 REMARK 500 4 PHE A 112 -99.32 -84.00 REMARK 500 4 GLN A 113 162.36 168.94 REMARK 500 4 ASN A 116 -38.73 -164.62 REMARK 500 4 CYS A 117 -129.08 -96.23 REMARK 500 4 SER A 118 69.74 159.88 REMARK 500 4 ARG A 124 110.77 176.13 REMARK 500 4 ARG A 126 8.27 -162.46 REMARK 500 4 ILE A 128 76.81 49.87 REMARK 500 4 ARG A 129 95.71 -29.57 REMARK 500 4 SER A 130 -68.57 -145.96 REMARK 500 4 LYS A 131 -60.70 -140.92 REMARK 500 REMARK 500 THIS ENTRY HAS 131 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 175 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 114 SG REMARK 620 2 CYS A 117 SG 114.2 REMARK 620 3 CYS A 136 SG 112.4 105.2 REMARK 620 4 CYS A 139 SG 111.3 105.7 107.3 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 175 DBREF 2KAE A 111 166 UNP Q9GSP3 Q9GSP3_CAEEL 111 166 DBREF 2KAE C 21 40 PDB 2KAE 2KAE 21 40 DBREF 2KAE B 1 20 PDB 2KAE 2KAE 1 20 SEQADV 2KAE GLY A 104 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE SER A 105 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE HIS A 106 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE MET A 107 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE ASN A 108 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE LYS A 109 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE LYS A 110 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE GLU A 167 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE THR A 168 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE ASN A 169 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE GLY A 170 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE VAL A 171 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE ASP A 172 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE SER A 173 UNP Q9GSP3 EXPRESSION TAG SEQADV 2KAE PHE A 174 UNP Q9GSP3 EXPRESSION TAG SEQRES 1 A 71 GLY SER HIS MET ASN LYS LYS SER PHE GLN CYS SER ASN SEQRES 2 A 71 CYS SER VAL THR GLU THR ILE ARG TRP ARG ASN ILE ARG SEQRES 3 A 71 SER LYS GLU GLY ILE GLN CYS ASN ALA CYS PHE ILE TYR SEQRES 4 A 71 GLN ARG LYS TYR ASN LYS THR ARG PRO VAL THR ALA VAL SEQRES 5 A 71 ASN LYS TYR GLN LYS ARG LYS LEU LYS VAL GLN GLU THR SEQRES 6 A 71 ASN GLY VAL ASP SER PHE SEQRES 1 C 20 DC DG DG DA DA DA DA DG DT DA DT DA DC SEQRES 2 C 20 DT DT DT DT DC DC DG SEQRES 1 B 20 DC DG DG DA DA DA DA DG DT DA DT DA DC SEQRES 2 B 20 DT DT DT DT DC DC DG HET ZN A 175 1 HETNAM ZN ZINC ION FORMUL 4 ZN ZN 2+ HELIX 1 1 ASN A 137 LYS A 148 1 12 HELIX 2 2 VAL A 152 LEU A 163 1 12 LINK SG CYS A 114 ZN ZN A 175 1555 1555 2.37 LINK SG CYS A 117 ZN ZN A 175 1555 1555 2.21 LINK SG CYS A 136 ZN ZN A 175 1555 1555 2.17 LINK SG CYS A 139 ZN ZN A 175 1555 1555 2.24 SITE 1 AC1 4 CYS A 114 CYS A 117 CYS A 136 CYS A 139 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