PDB Short entry for 1X0F HEADER TRANSCRIPTION/DNA 22-MAR-05 1X0F TITLE COMPLEX STRUCTURE OF THE C-TERMINAL RNA-BINDING DOMAIN OF HNRNP TITLE 2 D(AUF1) WITH TELOMERIC DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*TP*AP*GP*G)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN D0; COMPND 7 CHAIN: A; COMPND 8 FRAGMENT: C-TERMINAL RNA-BINDING DOMAIN; COMPND 9 SYNONYM: HNRNP D0, AU-RICH ELEMENT RNA-BINDING PROTEIN 1; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 5 ORGANISM_COMMON: HUMAN; SOURCE 6 ORGANISM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS RNA-BINDING DOMAIN, DNA-BINDING DOMAIN, RRM, HNRNP D, AUF1, TELOMERE, KEYWDS 2 COMPLEX, STRUCTURAL GENOMICS, TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.ENOKIZONO,Y.KONISHI,K.NAGATA,K.OUHASHI,S.UESUGI,F.ISHIKAWA, AUTHOR 2 M.KATAHIRA REVDAT 4 02-MAR-22 1X0F 1 REMARK REVDAT 3 24-FEB-09 1X0F 1 VERSN REVDAT 2 17-MAY-05 1X0F 2 JRNL REVDAT 1 05-APR-05 1X0F 0 JRNL AUTH Y.ENOKIZONO,Y.KONISHI,K.NAGATA,K.OUHASHI,S.UESUGI, JRNL AUTH 2 F.ISHIKAWA,M.KATAHIRA JRNL TITL STRUCTURE OF HNRNP D COMPLEXED WITH SINGLE-STRANDED TELOMERE JRNL TITL 2 DNA AND UNFOLDING OF THE QUADRUPLEX BY HETEROGENEOUS NUCLEAR JRNL TITL 3 RIBONUCLEOPROTEIN D. JRNL REF J.BIOL.CHEM. V. 280 18862 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15734733 JRNL DOI 10.1074/JBC.M411822200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.ENOKIZONO,Y.KONISHI,K.NAGATA,K.OUHASHI,S.UESUGI, REMARK 1 AUTH 2 F.ISHIKAWA,M.KATAHIRA REMARK 1 TITL STRUCTURE OF HNRNP D COMPLEXED WITH SINGLE-STRANDED TELOMERE REMARK 1 TITL 2 DNA AND UNFOLDING OF THE QUADRUPLEX BY HNRNP D REMARK 1 REF J.BIOL.CHEM. V. 280 2005 REMARK 1 REFN ESSN 1083-351X REMARK 1 PMID 15734733 REMARK 1 DOI 10.1074/JBC.M411822200 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.KATAHIRA,Y.MIYANOIRI,Y.ENOKIZONO,G.MATSUDA,T.NAGATA, REMARK 1 AUTH 2 F.ISHIKAWA,S.UESUGI REMARK 1 TITL STRUCTURE OF THE C-TERMINAL RNA-BINDING DOMAIN OF HNRNP D0 REMARK 1 TITL 2 (AUF1), ITS INTERACTIONS WITH RNA AND DNA, AND CHANGE IN REMARK 1 TITL 3 BACKBONE DYNAMICS UPON COMPLEX FORMATION WITH DNA REMARK 1 REF J.MOL.BIOL. V. 311 973 2001 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 11531333 REMARK 1 DOI 10.1006/JMBI.2001.4862 REMARK 1 REFERENCE 3 REMARK 1 AUTH T.NAGATA,Y.KURIHARA,G.MATSUDA,J.SAEKI,T.KOHNO,Y.YANAGIDA, REMARK 1 AUTH 2 F.ISHIKAWA,S.UESUGI,M.KATAHIRA REMARK 1 TITL STRUCTURE AND INTERACTIONS WITH RNA OF THE N-TERMINAL REMARK 1 TITL 2 UUAG-SPECIFIC RNA-BINDING DOMAIN OF HNRNP D0 REMARK 1 REF J.MOL.BIOL. V. 287 221 1999 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 10080887 REMARK 1 DOI 10.1006/JMBI.1999.2616 REMARK 1 REFERENCE 4 REMARK 1 AUTH F.ISHIKAWA,M.J.MATUNIS,G.DREYFUSS,T.R.CECH REMARK 1 TITL NUCLEAR PROTEINS THAT BIND THE PRE-MRNA 3' SPLICE SITE REMARK 1 TITL 2 SEQUENCE R(UUAG/G) AND THE HUMAN TELOMERIC DNA SEQUENCE REMARK 1 TITL 3 D(TTAGGG)N REMARK 1 REF MOL.CELL.BIOL. V. 13 4301 1993 REMARK 1 REFN ISSN 0270-7306 REMARK 1 PMID 8321232 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851, X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1X0F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000024222. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 100MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2MM U-13C, 15N HNRNP D BD2, REMARK 210 2.4MM DNA, 20MM SODIUM PHOSPHATE, REMARK 210 10MM DEUTERATED DTT, 1MM SODIUM REMARK 210 AZIDE; 2MM U-15N HNRNP D BD2, REMARK 210 2.4MM DNA, 20MM SODIUM PHOSPHATE, REMARK 210 10MM DEUTERATED DTT, 1MM SODIUM REMARK 210 AZIDE; 2MM HNRNP D BD2, 2.4MM REMARK 210 DNA, 20MM SODIUM PHOSPHATE, 10MM REMARK 210 DEUTERATED DTT, 1MM SODIUM AZIDE; REMARK 210 2MM U-13C, 15N HNRNP D BD2, REMARK 210 2.4MM DNA, 20MM SODIUM PHOSPHATE, REMARK 210 10MM DEUTERATED DTT, 1MM SODIUM REMARK 210 AZIDE; 2MM U-15N HNRNP D BD2, REMARK 210 2.4MM DNA, 20MM SODIUM PHOSPHATE, REMARK 210 10MM DEUTERATED DTT, 1MM SODIUM REMARK 210 AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_TOCSY; 4D_13C- REMARK 210 SEPARATED_NOESY; 3D HNHA; 3D REMARK 210 HNCA; HCCH-TOCSY; HCCH-COSY; 1H, REMARK 210 15N-HSQC; 2D_ROESY; 2D_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, XWINNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 228 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: THIS STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR AND 3D REMARK 210 HETERONUCLEAR TECHNIQUES. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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: 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 O GLU A 200 H GLY A 204 1.44 REMARK 500 HH TYR A 201 ND1 HIS A 245 1.45 REMARK 500 O GLY A 187 H GLU A 253 1.60 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 SER A 190 -177.41 -45.40 REMARK 500 1 ASP A 192 77.65 160.55 REMARK 500 1 GLU A 195 -17.81 -48.10 REMARK 500 1 LYS A 221 -179.22 -51.92 REMARK 500 1 VAL A 256 121.76 -32.87 REMARK 500 2 SER A 190 179.65 -45.31 REMARK 500 2 PRO A 191 4.98 -68.33 REMARK 500 2 ASP A 192 76.25 161.40 REMARK 500 2 LYS A 221 -178.67 -49.99 REMARK 500 2 VAL A 256 121.46 -32.84 REMARK 500 3 SER A 190 172.64 -42.27 REMARK 500 3 ASP A 192 73.19 172.78 REMARK 500 3 ASN A 220 46.74 38.17 REMARK 500 3 ARG A 222 46.70 -93.66 REMARK 500 3 VAL A 256 123.52 -33.38 REMARK 500 4 SER A 190 -175.17 -46.70 REMARK 500 4 ASP A 192 74.21 169.58 REMARK 500 4 ASN A 220 59.01 37.35 REMARK 500 4 LYS A 221 -179.62 -57.26 REMARK 500 4 ARG A 222 40.17 -99.48 REMARK 500 4 LEU A 249 -39.80 -133.39 REMARK 500 4 VAL A 256 123.54 -32.78 REMARK 500 5 SER A 190 -173.91 -44.68 REMARK 500 5 ASP A 192 78.24 158.20 REMARK 500 5 LYS A 221 177.16 -52.40 REMARK 500 5 LYS A 243 -81.92 -41.90 REMARK 500 5 VAL A 256 124.94 -33.23 REMARK 500 6 SER A 190 -173.66 -47.71 REMARK 500 6 ASP A 192 76.89 159.73 REMARK 500 6 ASN A 220 71.72 62.47 REMARK 500 6 LYS A 243 -75.53 -50.38 REMARK 500 6 VAL A 256 124.51 -33.20 REMARK 500 7 SER A 190 -177.45 -46.67 REMARK 500 7 ASP A 192 73.00 171.76 REMARK 500 7 PRO A 214 -156.59 -49.72 REMARK 500 7 THR A 219 11.24 -145.29 REMARK 500 7 ASN A 220 -87.82 -148.80 REMARK 500 7 ARG A 222 41.94 -88.13 REMARK 500 7 VAL A 256 124.46 -33.16 REMARK 500 8 SER A 190 -175.15 -46.72 REMARK 500 8 ASP A 192 74.72 161.86 REMARK 500 8 GLU A 195 -15.40 -48.00 REMARK 500 8 THR A 219 14.88 -150.24 REMARK 500 8 ASN A 220 96.76 37.70 REMARK 500 8 LYS A 243 -74.96 -39.98 REMARK 500 8 VAL A 256 121.78 -32.80 REMARK 500 9 SER A 190 -173.48 -48.50 REMARK 500 9 ASP A 192 78.19 157.58 REMARK 500 9 PRO A 214 -159.99 -48.45 REMARK 500 9 THR A 219 13.31 -146.99 REMARK 500 REMARK 500 THIS ENTRY HAS 121 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IQT RELATED DB: PDB REMARK 900 THE 20 STRUCTURES WITH THE LOWEST ENERGY OF THE C-TERMINAL RNA- REMARK 900 BINDING DOMAIN OF HNRNP D REMARK 900 RELATED ID: 1HD0 RELATED DB: PDB REMARK 900 THE MINIMIZED AVERAGE STRUCTURE OF THE N-TERMINAL RNA-BINDING REMARK 900 DOMAIN OF HNRNP D REMARK 900 RELATED ID: 1HD1 RELATED DB: PDB REMARK 900 THE STRUCTURES OF THE N-TERMINAL RNA-BINDING DOMAIN OF HNRNP D REMARK 900 RELATED ID: 1WTB RELATED DB: PDB REMARK 900 THE 20 STRUCTURES WITH THE LOWEST ENERGY OF THE C-TERMINAL RNA- REMARK 900 BINDING DOMAIN OF HNRNP D WITH D(TAGG) (DATABASE FOR TORSION ANGLES REMARK 900 NOT USED) DBREF 1X0F A 181 259 UNP Q14103 HNRPD_HUMAN 181 259 DBREF 1X0F B 2 5 PDB 1X0F 1X0F 2 5 SEQRES 1 B 4 DT DA DG DG SEQRES 1 A 79 VAL LYS LYS ILE PHE VAL GLY GLY LEU SER PRO ASP THR SEQRES 2 A 79 PRO GLU GLU LYS ILE ARG GLU TYR PHE GLY GLY PHE GLY SEQRES 3 A 79 GLU VAL GLU SER ILE GLU LEU PRO MET ASP ASN LYS THR SEQRES 4 A 79 ASN LYS ARG ARG GLY PHE CYS PHE ILE THR PHE LYS GLU SEQRES 5 A 79 GLU GLU PRO VAL LYS LYS ILE MET GLU LYS LYS TYR HIS SEQRES 6 A 79 ASN VAL GLY LEU SER LYS CYS GLU ILE LYS VAL ALA MET SEQRES 7 A 79 SER HELIX 1 1 GLU A 195 PHE A 205 1 11 HELIX 2 2 GLU A 233 GLU A 241 1 9 SHEET 1 A 5 TYR A 244 VAL A 247 0 SHEET 2 A 5 SER A 250 LYS A 255 -1 N CYS A 252 O HIS A 245 SHEET 3 A 5 LYS A 183 GLY A 188 -1 N PHE A 185 O LYS A 255 SHEET 4 A 5 PHE A 225 PHE A 230 -1 O CYS A 226 N VAL A 186 SHEET 5 A 5 VAL A 208 PRO A 214 -1 N GLU A 209 O THR A 229 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