1ITY - Header Asymmetric Unit

HEADER DNA BINDING PROTEIN 15-FEB-02 1ITY

TITLE SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN OF HUMAN TRF1

COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRF1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA BINDING DOMAIN; COMPND 5 SYNONYM: TELOMERIC REPEAT BINDING FACTOR 1; COMPND 6 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: TRF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET13A

KEYWDS HELIX-TURN-HELIX, TELOMERES, DNA BINDING, MYB DOMAIN, RIKEN KEYWDS 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL KEYWDS 3 GENOMICS, DNA BINDING PROTEIN

EXPDTA SOLUTION NMR

NUMMDL 25

AUTHOR T.NISHIKAWA,H.OKAMURA,A.NAGADOI,P.KONIG,D.RHODES, AUTHOR 2 Y.NISHIMURA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 3 (RSGI)

REVDAT 2 24-FEB-09 1ITY 1 VERSN REVDAT 1 06-MAR-02 1ITY 0

JRNL AUTH T.NISHIKAWA,H.OKAMURA,A.NAGADOI,P.KONIG,D.RHODES, JRNL AUTH 2 Y.NISHIMURA JRNL TITL SOLUTION STRUCTURE OF A TELOMERIC DNA COMPLEX OF JRNL TITL 2 HUMAN TRF1 JRNL REF STRUCTURE V. 9 1237 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11738049 JRNL DOI 10.1016/S0969-2126(01)00688-8

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : EMBOSS 5.0 REMARK 3 AUTHORS : NAKAI, T., KIDERA, A., AND NAKAMURA, H. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE GENERATED BY 4D REMARK 3 SIMULATED ANNEALING WITH EMBOSS, BASED ON A TOTAL OF 916 REMARK 3 EXPERIMENTAL RESTRAINTS, 852 ARE NOE-DERIVED DISTANCE REMARK 3 RESTRAINTS, 36 HYDROGEN RESTRAINTS AND 28 DIHEDRAL RESTRAINTS. REMARK 3 25 OUT OF 100 STRUCTURES WHICH HAVE THE LOWEST VIOLATION AND A REMARK 3 LOW ENERGIES WERE SELECTED FOR THE FINAL SET.

REMARK 4 REMARK 4 1ITY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-FEB-02. REMARK 100 THE RCSB ID CODE IS RCSB005271.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5-2.5MM TRF1 U-15N, 13C, REMARK 210 50MM PHOSPHATE BUFFER, 100MM REMARK 210 NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNHA, 3D HNHB, 3D REMARK 210 SEQUENTIAL ASSIGNMENT REMARK 210 PROTOCOL, 3D_15N_SEPARATED_ REMARK 210 NOESY, 3D_13C_SEPARATED_NOESY, REMARK 210 2D NOESY, 2D TOCSY, 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX, DRX, AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY/SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 2 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 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 1-25 REMARK 465 RES C SSSEQI REMARK 465 THR A 371 REMARK 465 PRO A 372

REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 14 ARG A 415 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES 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 374 71.33 -69.80 REMARK 500 1 HIS A 375 -35.50 172.92 REMARK 500 1 LYS A 379 118.64 74.15 REMARK 500 1 ASN A 402 53.91 -149.06 REMARK 500 1 ASN A 414 73.76 -154.73 REMARK 500 1 LYS A 431 43.96 -88.94 REMARK 500 1 LEU A 432 93.44 -11.48 REMARK 500 1 SER A 434 -135.51 56.50 REMARK 500 1 ASP A 436 24.80 -146.33 REMARK 500 2 ARG A 378 -100.16 49.38 REMARK 500 2 LYS A 379 36.39 -141.28 REMARK 500 2 GLN A 381 68.97 -69.74 REMARK 500 2 ALA A 382 52.75 -162.26 REMARK 500 2 TRP A 383 171.12 64.55 REMARK 500 2 ASN A 414 88.83 62.19 REMARK 500 2 LYS A 429 -72.25 -75.90 REMARK 500 2 LYS A 431 -21.59 179.55 REMARK 500 2 SER A 434 69.04 -153.77 REMARK 500 3 LYS A 374 -116.06 55.87 REMARK 500 3 HIS A 375 46.27 -157.35 REMARK 500 3 ARG A 376 173.25 71.55 REMARK 500 3 ARG A 378 -167.61 -179.39 REMARK 500 3 LYS A 379 129.63 -31.96 REMARK 500 3 ARG A 380 -168.57 -170.71 REMARK 500 3 TRP A 383 79.19 56.87 REMARK 500 3 ASN A 402 47.61 -76.21 REMARK 500 3 LEU A 432 62.09 67.09 REMARK 500 3 SER A 434 -86.45 -165.61 REMARK 500 3 SER A 435 -109.54 -122.72 REMARK 500 3 ASP A 436 -73.27 -150.02 REMARK 500 4 LYS A 374 -70.25 178.37 REMARK 500 4 HIS A 375 -175.09 59.94 REMARK 500 4 ARG A 376 115.29 66.27 REMARK 500 4 ARG A 380 98.54 -57.53 REMARK 500 4 ALA A 382 -131.83 55.19 REMARK 500 4 ASN A 414 83.50 61.31 REMARK 500 4 LEU A 430 -42.30 -178.15 REMARK 500 4 LYS A 431 -58.43 -19.11 REMARK 500 4 LEU A 432 32.30 -162.72 REMARK 500 5 ALA A 377 57.08 -162.56 REMARK 500 5 ARG A 380 34.71 -77.67 REMARK 500 5 ALA A 382 73.61 176.66 REMARK 500 5 LEU A 430 37.22 178.94 REMARK 500 5 LEU A 432 -56.14 -129.34 REMARK 500 5 ILE A 433 -87.06 -79.54 REMARK 500 6 ARG A 378 68.59 60.57 REMARK 500 6 TRP A 383 73.05 52.38 REMARK 500 6 ASN A 414 64.08 -161.02 REMARK 500 6 LYS A 431 -67.89 -159.55 REMARK 500 6 LEU A 432 -83.00 -169.73 REMARK 500 6 SER A 434 -159.49 -158.56 REMARK 500 6 SER A 435 -44.86 72.13 REMARK 500 7 HIS A 375 74.53 58.08 REMARK 500 7 ARG A 378 -59.22 72.37 REMARK 500 7 LYS A 379 120.65 74.30 REMARK 500 7 ALA A 382 -148.12 51.40 REMARK 500 7 ASN A 414 78.02 54.35 REMARK 500 7 SER A 434 69.74 -178.64 REMARK 500 7 GLU A 438 -75.34 111.12 REMARK 500 8 GLN A 381 -39.32 70.15 REMARK 500 8 SER A 435 36.87 -154.20 REMARK 500 9 HIS A 375 -79.34 -156.90 REMARK 500 9 ARG A 376 91.06 -164.91 REMARK 500 9 ARG A 380 -70.55 -85.72 REMARK 500 9 LYS A 431 -89.92 -85.21 REMARK 500 9 LEU A 432 31.41 175.53 REMARK 500 9 SER A 434 45.32 -178.86 REMARK 500 9 SER A 435 -74.68 70.21 REMARK 500 9 ASP A 436 67.64 21.78 REMARK 500 10 ARG A 376 -71.66 65.51 REMARK 500 10 ALA A 377 -157.64 60.48 REMARK 500 10 TRP A 383 112.79 71.26 REMARK 500 10 LEU A 432 66.08 65.50 REMARK 500 10 SER A 437 -145.37 -161.52 REMARK 500 11 HIS A 375 118.63 79.88 REMARK 500 11 ARG A 376 -38.29 73.55 REMARK 500 11 TRP A 383 99.57 70.61 REMARK 500 11 ASN A 402 46.08 -75.87 REMARK 500 11 LYS A 429 -66.24 -27.15 REMARK 500 11 LYS A 431 14.51 59.44 REMARK 500 11 ILE A 433 -46.76 -135.16 REMARK 500 11 SER A 435 176.42 72.19 REMARK 500 11 SER A 437 172.76 68.26 REMARK 500 11 GLU A 438 114.33 -162.00 REMARK 500 12 ARG A 376 108.11 74.47 REMARK 500 12 ARG A 378 -63.87 74.34 REMARK 500 12 LYS A 379 -167.20 176.65 REMARK 500 12 GLN A 381 117.72 79.54 REMARK 500 12 ALA A 382 48.48 -162.80 REMARK 500 12 TRP A 383 170.49 59.70 REMARK 500 12 ASN A 402 46.17 -76.43 REMARK 500 12 ASN A 414 93.72 65.96 REMARK 500 13 LYS A 379 -127.51 56.89 REMARK 500 13 ALA A 382 -138.46 61.17 REMARK 500 13 ASN A 402 41.84 -76.71 REMARK 500 13 LEU A 432 41.26 -87.85 REMARK 500 13 SER A 435 107.38 -19.19 REMARK 500 13 ASP A 436 -60.68 -27.88 REMARK 500 13 SER A 437 -77.05 -79.33 REMARK 500 14 ARG A 376 178.43 72.10 REMARK 500 14 ARG A 380 -168.11 -101.77 REMARK 500 14 ASN A 413 47.35 -75.74 REMARK 500 14 ASN A 414 87.41 77.65 REMARK 500 14 LEU A 432 65.35 60.46 REMARK 500 14 SER A 434 63.76 66.49 REMARK 500 14 GLU A 438 165.79 69.83 REMARK 500 15 LYS A 374 56.47 79.44 REMARK 500 15 HIS A 375 -69.43 75.81 REMARK 500 15 ARG A 376 176.09 65.85 REMARK 500 15 LYS A 379 142.33 77.31 REMARK 500 15 ALA A 382 -158.71 -77.96 REMARK 500 15 ASN A 402 49.46 -78.25 REMARK 500 15 ASN A 414 42.83 -164.93 REMARK 500 15 LYS A 429 25.78 -75.75 REMARK 500 15 LEU A 432 -50.04 -145.41 REMARK 500 16 LYS A 374 151.47 68.57 REMARK 500 16 ARG A 376 48.54 -156.38 REMARK 500 16 ARG A 378 75.21 -158.05 REMARK 500 16 ASN A 402 45.93 -149.49 REMARK 500 16 ASN A 414 72.14 -158.33 REMARK 500 16 LEU A 430 51.56 -179.78 REMARK 500 16 LYS A 431 -91.93 -116.31 REMARK 500 16 SER A 435 -144.82 87.94 REMARK 500 16 SER A 437 131.17 121.78 REMARK 500 17 HIS A 375 -92.76 -78.17 REMARK 500 17 ARG A 376 -67.88 -152.06 REMARK 500 17 ALA A 377 -13.40 -148.67 REMARK 500 17 ARG A 380 -61.84 -120.63 REMARK 500 17 GLN A 381 -80.82 -141.51 REMARK 500 17 ALA A 382 -153.87 -123.59 REMARK 500 17 TRP A 383 69.34 73.51 REMARK 500 17 LEU A 430 33.63 -170.58 REMARK 500 17 LEU A 432 -54.24 -167.12 REMARK 500 17 ILE A 433 95.79 -69.95 REMARK 500 17 SER A 435 -94.90 65.81 REMARK 500 17 SER A 437 -110.15 30.69 REMARK 500 17 GLU A 438 -42.76 164.64 REMARK 500 18 LYS A 374 -68.45 -136.02 REMARK 500 18 ARG A 380 126.64 72.00 REMARK 500 18 GLN A 381 -48.43 73.07 REMARK 500 18 ASN A 402 43.45 -74.42 REMARK 500 18 TYR A 410 -154.19 -97.83 REMARK 500 18 LYS A 431 37.67 84.71 REMARK 500 18 ASP A 436 -146.77 53.42 REMARK 500 18 SER A 437 -75.38 -86.10 REMARK 500 19 HIS A 375 65.72 -118.08 REMARK 500 19 ARG A 376 48.25 -150.94 REMARK 500 19 LYS A 379 35.00 -73.75 REMARK 500 19 GLN A 381 44.44 -81.21 REMARK 500 19 ALA A 382 -172.55 54.80 REMARK 500 19 ASN A 402 46.74 -75.56 REMARK 500 19 ASN A 414 85.10 66.14 REMARK 500 19 LEU A 430 40.45 -165.45 REMARK 500 19 LYS A 431 -71.81 -91.22 REMARK 500 19 LEU A 432 41.10 -173.79 REMARK 500 19 SER A 437 34.26 -150.60 REMARK 500 20 LYS A 374 -166.12 64.26 REMARK 500 20 ARG A 380 -48.65 -163.38 REMARK 500 20 GLN A 381 -4.05 -55.55 REMARK 500 20 ALA A 382 -162.60 -71.74 REMARK 500 20 ASN A 414 83.54 -168.15 REMARK 500 20 LEU A 432 84.40 75.91 REMARK 500 20 ILE A 433 109.82 -29.42 REMARK 500 20 SER A 434 119.43 -175.15 REMARK 500 21 LYS A 374 -63.39 76.08 REMARK 500 21 GLN A 381 29.27 -148.31 REMARK 500 21 ASN A 414 68.98 62.61 REMARK 500 21 ASP A 436 -72.10 -91.14 REMARK 500 21 SER A 437 41.51 -153.71 REMARK 500 22 HIS A 375 -78.39 -85.71 REMARK 500 22 ARG A 376 -61.21 -171.55 REMARK 500 22 LYS A 379 -66.52 -125.49 REMARK 500 22 TRP A 383 89.16 52.20 REMARK 500 22 ASN A 402 48.77 -76.75 REMARK 500 22 ASN A 413 -61.12 -91.39 REMARK 500 22 ASN A 414 39.56 -156.55 REMARK 500 22 LEU A 432 88.38 63.57 REMARK 500 22 ILE A 433 93.72 -45.83 REMARK 500 22 GLU A 438 -65.74 -161.94 REMARK 500 23 LYS A 374 -73.00 66.80 REMARK 500 23 ARG A 378 81.79 54.93 REMARK 500 23 LYS A 379 -77.05 -83.95 REMARK 500 23 ARG A 380 161.34 70.49 REMARK 500 23 ASN A 402 45.04 -76.67 REMARK 500 23 LEU A 430 -77.49 -61.04 REMARK 500 23 LYS A 431 -48.88 -173.42 REMARK 500 23 LEU A 432 -62.52 -28.91 REMARK 500 24 ARG A 376 63.91 61.42 REMARK 500 24 ARG A 380 96.10 55.31 REMARK 500 24 ASN A 413 -74.74 -69.92 REMARK 500 24 LYS A 429 41.19 -84.21 REMARK 500 24 LEU A 430 -43.69 -147.05 REMARK 500 24 LYS A 431 -13.24 123.78 REMARK 500 24 LEU A 432 46.96 -80.31 REMARK 500 24 SER A 437 75.08 -151.78 REMARK 500 25 LYS A 374 132.14 -170.98 REMARK 500 25 HIS A 375 -67.17 -165.16 REMARK 500 25 LYS A 379 -43.96 -164.19 REMARK 500 25 ARG A 380 -53.57 -143.59 REMARK 500 25 TRP A 383 85.77 70.16 REMARK 500 25 ASN A 402 49.07 -76.29 REMARK 500 25 LYS A 431 -21.74 101.52 REMARK 500 25 SER A 434 -56.68 -154.47 REMARK 500 25 SER A 435 162.42 104.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 12 ARG A 376 0.17 SIDE_CHAIN REMARK 500 15 ARG A 415 0.12 SIDE_CHAIN REMARK 500 18 ARG A 378 0.09 SIDE_CHAIN REMARK 500 22 ARG A 423 0.11 SIDE_CHAIN REMARK 500 24 ARG A 423 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BA5 RELATED DB: PDB REMARK 900 1BA5 CONTAINS THE SAME PROTEIN TRUNCATED IN N- AND C- REMARK 900 TERMINI. REMARK 900 RELATED ID: MY_001000018.1 RELATED DB: TARGETDB

DBREF 1ITY A 371 439 UNP P54274 TERF1_HUMAN 371 439

SEQRES 1 A 69 THR PRO GLU LYS HIS ARG ALA ARG LYS ARG GLN ALA TRP SEQRES 2 A 69 LEU TRP GLU GLU ASP LYS ASN LEU ARG SER GLY VAL ARG SEQRES 3 A 69 LYS TYR GLY GLU GLY ASN TRP SER LYS ILE LEU LEU HIS SEQRES 4 A 69 TYR LYS PHE ASN ASN ARG THR SER VAL MET LEU LYS ASP SEQRES 5 A 69 ARG TRP ARG THR MET LYS LYS LEU LYS LEU ILE SER SER SEQRES 6 A 69 ASP SER GLU ASP

HELIX 1 1 LEU A 384 GLY A 399 1 16 HELIX 2 2 ASN A 402 TYR A 410 1 9 HELIX 3 3 THR A 416 LEU A 430 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