10 20 30 40 50 60 70 80 1VFC - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL PROTEIN/DNA 12-APR-04 1VFC
TITLE SOLUTION STRUCTURE OF THE DNA COMPLEX OF HUMAN TRF2
COMPND MOL_ID: 1; COMPND 2 MOLECULE: TELOMERIC REPEAT BINDING FACTOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA BINDING DOMAIN; COMPND 5 SYNONYM: TRF2, TTAGGG REPEAT BINDING FACTOR 2, TELOMERIC COMPND 6 DNA BINDING PROTEIN; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SHORT G-RICH STRAND; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: SHORT C-RICH STARND; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET23B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
KEYWDS MYB, HELIX-TURN-HELIX, TELOMERE, PROTEIN-DNA COMPLEX, KEYWDS 2 STRUCTURAL PROTEIN/DNA COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR Y.NISHIMURA,S.HANAOKA
REVDAT 2 24-FEB-09 1VFC 1 VERSN REVDAT 1 17-MAY-05 1VFC 0
JRNL AUTH S.HANAOKA,A.NAGADOI,Y.NISHIMURA JRNL TITL COMPARISON BETWEEN TRF2 AND TRF1 OF THEIR JRNL TITL 2 TELOMERIC DNA-BOUND STRUCTURES AND DNA-BINDING JRNL TITL 3 ACTIVITIES JRNL REF PROTEIN SCI. V. 14 119 2005 JRNL REFN ISSN 0961-8368 JRNL PMID 15608118 JRNL DOI 10.1110/PS.04983705
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, REMARK 3 RICE,SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 1450 RESTRAINTS, 1412 ARE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 38 DIHEDRAL ANGLE RESTRAINTS.
REMARK 4 REMARK 4 1VFC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-APR-04. REMARK 100 THE RCSB ID CODE IS RCSB006555.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 0.005M REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0-1.5MM TRF2 LABELED WITH REMARK 210 15N AND 13C, AND DNA; 5MM REMARK 210 POTASSIUM PHOSPHATE BUFFER, REMARK 210 90% H2O, 10% D2O; 1.0-1.5MM REMARK 210 TRF2 LABELED WITH 15N,AND DNA; REMARK 210 5MM POTASSIUM PHOSPHATE REMARK 210 BUFFER, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY, 3D REMARK 210 13C-EDITED(F1), 13C- REMARK 210 FILTERED(F3) NOESY, 3D 15N- REMARK 210 EDITED(F2), 15N/13C- REMARK 210 FILTERED(F3) NOESY, 3D_13C- REMARK 210 SEPARATED_TOCSY, 3D_13C- REMARK 210 SEPARATED_COSY, 3D_15N- REMARK 210 SEPARATED_NOESY, HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX, AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.0, SPARKY 3.98, CNS REMARK 210 1.0 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 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 : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY.
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 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 ASP A 439 108.77 59.82 REMARK 500 1 THR A 441 -77.32 -141.38 REMARK 500 1 ASN A 443 109.90 62.68 REMARK 500 1 THR A 445 83.22 -158.26 REMARK 500 1 ASN A 469 69.92 -102.65 REMARK 500 1 VAL A 480 -69.39 -122.89 REMARK 500 1 ASN A 481 56.54 -118.98 REMARK 500 2 ASP A 439 30.44 -150.02 REMARK 500 2 THR A 441 -51.18 -161.49 REMARK 500 2 ASN A 443 144.39 62.81 REMARK 500 2 LYS A 446 -142.60 -115.71 REMARK 500 3 SER A 440 177.37 63.11 REMARK 500 3 THR A 441 -78.00 -171.10 REMARK 500 3 THR A 445 32.01 -143.15 REMARK 500 3 ASN A 469 71.66 -102.95 REMARK 500 3 VAL A 480 -69.40 -127.64 REMARK 500 3 ASN A 481 57.04 -113.58 REMARK 500 4 ASP A 439 30.98 -141.08 REMARK 500 4 THR A 441 -66.32 -152.28 REMARK 500 4 ASN A 443 153.70 61.37 REMARK 500 4 THR A 445 84.68 62.56 REMARK 500 4 LYS A 446 -78.85 -78.73 REMARK 500 4 LYS A 447 -48.24 -134.72 REMARK 500 4 GLN A 448 42.07 -160.53 REMARK 500 4 ASN A 469 68.68 -100.54 REMARK 500 4 PRO A 478 48.80 -75.09 REMARK 500 4 ASN A 481 53.98 -100.13 REMARK 500 5 THR A 441 -72.50 -156.83 REMARK 500 5 ASN A 443 177.40 58.90 REMARK 500 5 THR A 445 88.85 -157.38 REMARK 500 5 LYS A 446 -111.18 -97.90 REMARK 500 5 ASN A 469 72.45 -103.35 REMARK 500 6 SER A 440 138.31 64.18 REMARK 500 6 THR A 441 -64.75 -142.86 REMARK 500 6 ASN A 443 114.31 60.67 REMARK 500 6 ILE A 444 112.77 -160.08 REMARK 500 6 LYS A 447 102.33 -164.81 REMARK 500 7 SER A 440 130.73 63.76 REMARK 500 7 THR A 441 -73.85 -127.50 REMARK 500 7 ASN A 443 157.15 63.30 REMARK 500 7 THR A 445 86.69 53.88 REMARK 500 7 TRP A 450 175.61 48.65 REMARK 500 7 ASN A 469 69.92 -102.72 REMARK 500 8 THR A 441 -50.47 -162.23 REMARK 500 8 ASN A 443 80.64 69.51 REMARK 500 8 ILE A 444 95.21 40.24 REMARK 500 8 THR A 445 151.70 61.84 REMARK 500 8 LYS A 446 33.25 -166.37 REMARK 500 8 TRP A 450 174.93 48.20 REMARK 500 8 ASN A 469 73.46 -102.81 REMARK 500 8 PRO A 478 60.61 -67.33 REMARK 500 8 VAL A 480 -70.65 -118.09 REMARK 500 9 THR A 441 -75.72 -155.55 REMARK 500 9 ILE A 444 -56.25 75.89 REMARK 500 9 GLN A 448 78.48 -108.50 REMARK 500 9 ASN A 469 76.41 -100.32 REMARK 500 10 THR A 441 -71.75 -168.98 REMARK 500 10 THR A 442 37.27 -97.82 REMARK 500 10 THR A 445 -172.96 -178.19 REMARK 500 10 LYS A 446 132.40 63.64 REMARK 500 10 TRP A 450 -84.33 -51.75 REMARK 500 10 THR A 451 172.94 161.75 REMARK 500 10 ASN A 481 27.69 49.46 REMARK 500 11 ASP A 439 110.21 61.70 REMARK 500 11 THR A 441 -43.56 -167.22 REMARK 500 11 ASN A 443 164.05 58.86 REMARK 500 11 THR A 445 75.21 -104.93 REMARK 500 11 TRP A 450 -86.54 -57.95 REMARK 500 11 THR A 451 175.09 173.28 REMARK 500 11 ASN A 469 72.17 -102.23 REMARK 500 11 PRO A 478 49.93 -79.01 REMARK 500 11 VAL A 480 -68.47 -121.22 REMARK 500 11 ASN A 481 68.63 -117.61 REMARK 500 12 THR A 441 -55.24 -147.55 REMARK 500 12 ASN A 443 121.64 63.81 REMARK 500 12 ILE A 444 94.48 34.41 REMARK 500 12 THR A 445 46.85 -158.05 REMARK 500 12 LYS A 446 -57.91 -143.36 REMARK 500 12 TRP A 450 176.35 46.76 REMARK 500 12 ASN A 469 68.36 -100.54 REMARK 500 13 SER A 440 148.38 62.29 REMARK 500 13 THR A 441 -73.57 -176.56 REMARK 500 13 ASN A 443 148.91 167.75 REMARK 500 13 LYS A 446 -73.62 -88.83 REMARK 500 14 THR A 441 -58.28 -162.18 REMARK 500 14 ASN A 443 158.61 60.10 REMARK 500 14 LYS A 446 128.22 -175.50 REMARK 500 14 TRP A 450 175.74 49.35 REMARK 500 14 ASN A 469 69.64 -102.92 REMARK 500 14 PRO A 478 59.47 -68.41 REMARK 500 15 THR A 441 -60.98 -170.89 REMARK 500 15 ASN A 443 171.14 66.90 REMARK 500 15 ILE A 444 84.27 -64.63 REMARK 500 15 LYS A 446 -56.34 -126.58 REMARK 500 15 TRP A 450 175.21 48.82 REMARK 500 15 ASN A 469 70.77 -101.57 REMARK 500 15 PRO A 478 62.89 -67.48 REMARK 500 16 THR A 441 -48.93 -163.08 REMARK 500 16 ASN A 443 115.44 61.11 REMARK 500 16 THR A 445 85.02 65.19 REMARK 500 16 PRO A 478 61.28 -68.07 REMARK 500 17 THR A 441 -60.06 -158.07 REMARK 500 17 ASN A 443 109.50 58.95 REMARK 500 17 LYS A 446 130.86 179.43 REMARK 500 17 LYS A 447 79.09 61.63 REMARK 500 17 ASN A 481 28.30 49.66 REMARK 500 18 THR A 441 -71.68 -142.70 REMARK 500 18 ASN A 443 103.84 59.34 REMARK 500 18 LYS A 446 33.34 -167.59 REMARK 500 18 GLN A 448 73.51 -102.28 REMARK 500 18 ASN A 469 68.48 -101.86 REMARK 500 18 PRO A 478 61.72 -67.93 REMARK 500 19 THR A 441 -50.00 -176.80 REMARK 500 19 ASN A 443 -174.28 59.23 REMARK 500 19 LYS A 446 -151.09 -121.41 REMARK 500 19 TRP A 450 175.99 47.91 REMARK 500 19 ASN A 469 66.72 -102.33 REMARK 500 19 VAL A 480 -71.63 -81.40 REMARK 500 19 ASN A 481 52.99 -99.80 REMARK 500 20 ASP A 439 83.02 59.91 REMARK 500 20 THR A 441 -69.45 -130.77 REMARK 500 20 ASN A 443 131.28 69.48 REMARK 500 20 ILE A 444 -20.40 85.20 REMARK 500 20 THR A 445 154.04 61.69 REMARK 500 20 LYS A 446 -52.25 -141.53 REMARK 500 20 LYS A 449 58.98 -90.17 REMARK 500 20 TRP A 450 175.92 48.49 REMARK 500 20 ASN A 469 70.80 -103.14 REMARK 500 20 PRO A 478 57.21 -69.81 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VF9 RELATED DB: PDB REMARK 900 HUMAN TRF2
DBREF 1VFC A 438 500 UNP Q15554 TERF2_HUMAN 438 500 DBREF 1VFC B 1 13 PDB 1VFC 1VFC 1 13 DBREF 1VFC C 14 26 PDB 1VFC 1VFC 14 26
SEQRES 1 A 63 GLU ASP SER THR THR ASN ILE THR LYS LYS GLN LYS TRP SEQRES 2 A 63 THR VAL GLU GLU SER GLU TRP VAL LYS ALA GLY VAL GLN SEQRES 3 A 63 LYS TYR GLY GLU GLY ASN TRP ALA ALA ILE SER LYS ASN SEQRES 4 A 63 TYR PRO PHE VAL ASN ARG THR ALA VAL MET ILE LYS ASP SEQRES 5 A 63 ARG TRP ARG THR MET LYS ARG LEU GLY MET ASN SEQRES 1 B 13 DG DT DT DA DG DG DG DT DT DA DG DG DG SEQRES 1 C 13 DC DC DC DT DA DA DC DC DC DT DA DA DC
HELIX 1 1 THR A 451 TYR A 465 1 15 HELIX 2 2 ASN A 469 TYR A 477 1 9 HELIX 3 3 THR A 483 LEU A 497 1 15
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