PDB Short entry for 2MKN HEADER RNA BINDING PROTEIN/RNA 10-FEB-14 2MKN TITLE STRUCTURAL CHARACTERIZATION OF INTERACTIONS BETWEEN THE DOUBLE- TITLE 2 STRANDED RNA-BINDING ZINC FINGER PROTEIN JAZ AND DSRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER PROTEIN 346; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 181-224; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'- COMPND 8 R(*GP*CP*CP*GP*UP*GP*GP*UP*CP*UP*GP*GP*UP*GP*GP*CP*CP*GP*G)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA (5'- COMPND 13 R(P*CP*CP*GP*GP*CP*CP*AP*CP*CP*AP*GP*AP*CP*CP*AP*CP*GP*GP*C)-3'); COMPND 14 CHAIN: C; COMPND 15 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: ZNF346, JAZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630 KEYWDS ZINC FINGER, DSRNA-BINDING, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR AUTHOR P.WRIGHT,J.DYSON,R.BURGE,M.MARTINEZ-YAMOUT REVDAT 3 27-APR-16 2MKN 1 ATOM REMARK SEQRES DBREF REVDAT 3 2 1 SOURCE REVDAT 2 26-MAR-14 2MKN 1 JRNL REVDAT 1 19-MAR-14 2MKN 0 JRNL AUTH R.G.BURGE,M.A.MARTINEZ-YAMOUT,H.J.DYSON,P.E.WRIGHT JRNL TITL STRUCTURAL CHARACTERIZATION OF INTERACTIONS BETWEEN THE JRNL TITL 2 DOUBLE-STRANDED RNA-BINDING ZINC FINGER PROTEIN JAZ AND JRNL TITL 3 NUCLEIC ACIDS. JRNL REF BIOCHEMISTRY V. 53 1495 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 24521053 JRNL DOI 10.1021/BI401675H REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, HADDOCK REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER), ALEXANDRE REMARK 3 BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HADDOCK MODEL OF JAZ ZINC FINGER 3 REMARK 3 COMPLEXED WITH DSRNA. REMARK 4 REMARK 4 2MKN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-14. REMARK 100 THE RCSB ID CODE IS RCSB103728. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 55 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 200-300 MM [U-95% 13C; U-95% REMARK 210 15N] PROTEIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D HNCA; 3D HNCO; 3D HNCACB; 3D REMARK 210 1H-15N TOCSY; 3D 1H-13C NOESY; 3D REMARK 210 HCCH-COSY; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, NMRVIEW, TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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, B, C 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 400 REMARK 400 COMPOUND REMARK 400 THE HADDOCK STARTING RNA STRUCTURE IS AN IDEALIZED A-FORM HELIX AND REMARK 400 WAS GENERATED FROM THE MAKE-NA SERVER. 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 RES C SSSEQI REMARK 465 SER A 168 REMARK 465 THR A 169 REMARK 465 LYS A 170 REMARK 465 VAL A 171 REMARK 465 GLU A 172 REMARK 465 ALA A 173 REMARK 465 LEU A 174 REMARK 465 HIS A 175 REMARK 465 GLN A 176 REMARK 465 ASN A 177 REMARK 465 ARG A 178 REMARK 465 GLU A 179 REMARK 465 MET A 180 REMARK 465 LEU A 225 REMARK 465 ALA A 226 REMARK 465 ASP A 227 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 HIS A 209 -48.77 179.80 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 209 ND1 REMARK 620 2 HIS A 203 NE2 117.3 REMARK 620 3 CYS A 187 SG 101.8 107.4 REMARK 620 N 1 2 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 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2MKD RELATED DB: PDB REMARK 900 HADDOCK STARTING STRUCTURE REMARK 900 RELATED ID: 17679 RELATED DB: BMRB DBREF 2MKN A 168 227 UNP Q9UL40 ZN346_HUMAN 168 227 DBREF 2MKN B 1 19 PDB 2MKN 2MKN 1 19 DBREF 2MKN C 20 38 PDB 2MKN 2MKN 20 38 SEQRES 1 A 60 SER THR LYS VAL GLU ALA LEU HIS GLN ASN ARG GLU MET SEQRES 2 A 60 ILE ASP PRO ASP LYS PHE CYS SER LEU CYS HIS ALA THR SEQRES 3 A 60 PHE ASN ASP PRO VAL MET ALA GLN GLN HIS TYR VAL GLY SEQRES 4 A 60 LYS LYS HIS ARG LYS GLN GLU THR LYS LEU LYS LEU MET SEQRES 5 A 60 ALA ARG TYR GLY ARG LEU ALA ASP SEQRES 1 B 19 G C C G U G G U C U G G U SEQRES 2 B 19 G G C C G G SEQRES 1 C 19 C C G G C C A C C A G A C SEQRES 2 C 19 C A C G G C HET ZN A 301 1 HETNAM ZN ZINC ION FORMUL 4 ZN ZN 2+ HELIX 1 1 ASP A 196 VAL A 205 1 10 HELIX 2 2 GLY A 206 GLY A 223 1 18 SHEET 1 A 2 LYS A 185 PHE A 186 0 SHEET 2 A 2 THR A 193 PHE A 194 -1 O PHE A 194 N LYS A 185 LINK ND1 HIS A 209 ZN ZN A 301 1555 1555 1.78 LINK NE2 HIS A 203 ZN ZN A 301 1555 1555 1.79 LINK SG CYS A 187 ZN ZN A 301 1555 1555 2.03 SITE 1 AC1 4 CYS A 187 CYS A 190 HIS A 203 HIS A 209 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