Header list of 1wtb.pdb file
Complete list - r 2 2 Bytes
HEADER TRANSCRIPTION/DNA 22-NOV-04 1WTB
TITLE COMPLEX STRUCTURE OF THE C-TERMINAL RNA-BINDING DOMAIN OF HNRNP D
TITLE 2 (AUF1) WITH TELOMERE 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: AUF1, 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 5 02-MAR-22 1WTB 1 REMARK
REVDAT 4 24-FEB-09 1WTB 1 VERSN
REVDAT 3 03-JAN-06 1WTB 3 ATOM
REVDAT 2 03-JAN-06 1WTB 1 JRNL
REVDAT 1 05-APR-05 1WTB 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 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 2
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 3
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 1WTB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-NOV-04.
REMARK 100 THE DEPOSITION ID IS D_1000023975.
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; 3D_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 : 200
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 STANDARD 2D
REMARK 210 HOMONUCLEAR AND 3D 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 1.41
REMARK 500 O LYS A 243 H ILE A 254 1.43
REMARK 500 H GLU A 209 O THR A 229 1.46
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 LYS A 182 -35.11 -150.14
REMARK 500 1 LYS A 183 -167.46 -102.55
REMARK 500 1 LEU A 189 -143.04 -177.24
REMARK 500 1 PRO A 191 -35.90 -28.65
REMARK 500 1 ASP A 192 56.23 -151.36
REMARK 500 1 THR A 193 123.23 -39.40
REMARK 500 1 PRO A 194 99.11 -48.79
REMARK 500 1 GLU A 195 -19.59 -47.45
REMARK 500 1 TYR A 201 -39.16 -39.75
REMARK 500 1 PRO A 214 -158.08 -48.95
REMARK 500 1 MET A 215 125.11 158.61
REMARK 500 1 ASP A 216 71.78 -62.73
REMARK 500 1 LYS A 221 -156.43 -119.35
REMARK 500 1 ARG A 223 -106.36 4.37
REMARK 500 1 PHE A 225 -128.95 -135.40
REMARK 500 1 GLU A 232 -157.64 -90.85
REMARK 500 1 LYS A 243 -50.17 -14.72
REMARK 500 1 ASN A 246 74.28 -113.26
REMARK 500 1 VAL A 256 99.07 -37.41
REMARK 500 1 ALA A 257 -171.57 -44.98
REMARK 500 1 MET A 258 144.06 171.76
REMARK 500 2 LYS A 182 -34.83 -151.86
REMARK 500 2 LEU A 189 -144.80 -173.33
REMARK 500 2 PRO A 191 -37.68 -28.77
REMARK 500 2 ASP A 192 54.23 -151.40
REMARK 500 2 THR A 193 123.87 -39.87
REMARK 500 2 PRO A 194 101.95 -51.20
REMARK 500 2 PRO A 214 -167.22 -47.81
REMARK 500 2 MET A 215 120.80 154.67
REMARK 500 2 ASP A 216 85.19 -35.43
REMARK 500 2 THR A 219 -13.19 -143.24
REMARK 500 2 LYS A 221 -155.30 -117.90
REMARK 500 2 ARG A 223 -93.40 10.87
REMARK 500 2 PHE A 225 -121.73 -144.27
REMARK 500 2 LYS A 231 -37.13 -39.33
REMARK 500 2 GLU A 232 -155.56 -89.09
REMARK 500 2 GLU A 233 -0.93 -142.33
REMARK 500 2 LYS A 243 -50.08 -15.53
REMARK 500 2 VAL A 256 116.57 -34.52
REMARK 500 2 MET A 258 -151.25 -152.34
REMARK 500 3 LYS A 182 -34.90 -151.20
REMARK 500 3 ILE A 184 111.77 -166.45
REMARK 500 3 LEU A 189 -142.51 -174.07
REMARK 500 3 PRO A 191 -33.04 -31.96
REMARK 500 3 ASP A 192 53.34 -150.99
REMARK 500 3 PRO A 194 94.28 -52.01
REMARK 500 3 PRO A 214 -167.54 -50.51
REMARK 500 3 MET A 215 138.27 160.09
REMARK 500 3 ASP A 216 82.14 -63.53
REMARK 500 3 THR A 219 -26.91 -152.30
REMARK 500
REMARK 500 THIS ENTRY HAS 402 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 ENAGEY 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 20 STRUCTURES OF THE N-TERMINAL RNA-BINDING DOMAIN OF HNRNP D
DBREF 1WTB A 181 259 UNP Q14103 HNRPD_HUMAN 181 259
DBREF 1WTB B 2 5 PDB 1WTB 1WTB 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
MODEL 1
Complete list - r 2 2 Bytes