PDB Short entry for 2LF8 HEADER TRANSCRIPTION 28-JUN-11 2LF8 TITLE INTRAMOLECULAR REGULATION OF THE ETS DOMAIN WITHIN ETV6 SEQUENCE R335 TITLE 2 TO R458 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR ETV6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ETS DNA BINDING DOMAIN RESIDUES 335-458; COMPND 5 SYNONYM: ETS TRANSLOCATION VARIANT 6, ETS-RELATED PROTEIN TEL1, TEL; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: ETV6, MOUSE ETV6, TEL, TEL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28B+ KEYWDS AUTO-INHIBITION, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 19 AUTHOR H.COYNE III,S.M.GREEN,B.J.GRAVES,L.P.MCINTOSH REVDAT 3 14-JUN-23 2LF8 1 REMARK SEQADV REVDAT 2 25-JUL-12 2LF8 1 JRNL REVDAT 1 23-MAY-12 2LF8 0 JRNL AUTH H.J.COYNE,S.DE,M.OKON,S.M.GREEN,N.BHACHECH,B.J.GRAVES, JRNL AUTH 2 L.P.MCINTOSH JRNL TITL AUTOINHIBITION OF ETV6 (TEL) DNA BINDING: APPENDED HELICES JRNL TITL 2 STERICALLY BLOCK THE ETS DOMAIN. JRNL REF J.MOL.BIOL. V. 421 67 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22584210 JRNL DOI 10.1016/J.JMB.2012.05.010 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3, ARIA REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ITERATION PROTOCOL USED DEFAULT VALUES REMARK 3 EXCEPT ITERATION6 HAD THE VIOLATION TOLERANCE 0.09 VIOLATION REMARK 3 THRESHOLD 0.5 AND MAX_CONTRIBUTION 15, ITERATION7 SET THE REMARK 3 VIOLATION THRESHOLD 0.07 VIOLATION THRESHOLD 0.4 MAX_ REMARK 3 CONTRIBUTIONS 10. ITERATION 8 SET THE VIOLATION TOLERANCE 0.05 REMARK 3 VIOLATION THRESHOLD 0.3 MAX_CONTRIBUTIONS 5. THE CHEMICAL SHIFT REMARK 3 TOLERANCES WERE SET TO PROTON1=0.03 HETERO1=0.4 PROTON2=0.3 AND REMARK 3 HETERO2= 0.4. VIOLATED RESTRAINTS USED IN THE CALCUATION WERE REMARK 3 EXAMINED MANUALLY FOR CORRECT IDENTIFICATION AS WERE RESTRAINTS REMARK 3 NOT USED IN THE CALCULATION OVER 3 ANGSTROMS. LONG, MEDIUM, AND REMARK 3 SHORT NOES NOT USED IN THE CALCUALTION WERE EXAMINED ON REMARK 3 REFINEMENT AS WERE AMBIGOUS ASSIGMENTS WITH 3 OR MORE REMARK 3 CONTRIBUTIONS. REMARK 4 REMARK 4 2LF8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000102319. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5.8 REMARK 210 IONIC STRENGTH : 0.250 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 50 MM SODIUM PHOSPHATE, 200 MM REMARK 210 SODIUM CHLORIDE, 0.4 MM [U-99% REMARK 210 13C; U-99% 15N] PROTEIN, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-13C NOESY; REMARK 210 2D 1H-13C HSQC AROMATIC; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HCCH- REMARK 210 TOCSY; 3D HN(CO)CA; 3D HNCO; 3D REMARK 210 HBHA(CO)NH; DIPSI3DN; CMETHYL REMARK 210 NOESY; NMETHYL NOESY; REMARK 210 HCCTOCSYNNH; CCCTOCSYNNH; 2D 1H- REMARK 210 13C HSQC ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TALOS+, SPARKY, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 19 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 H1 GLY A 331 OE1 GLU A 431 1.57 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 332 -71.32 69.73 REMARK 500 1 THR A 383 -87.50 -85.53 REMARK 500 1 ARG A 410 -87.15 -83.41 REMARK 500 1 MET A 423 11.23 -68.65 REMARK 500 1 TYR A 443 41.26 -78.49 REMARK 500 1 PRO A 448 91.16 -60.49 REMARK 500 1 PRO A 453 94.98 -54.05 REMARK 500 1 VAL A 454 -74.67 -128.68 REMARK 500 2 ARG A 335 42.63 -159.81 REMARK 500 2 THR A 383 -82.83 -99.18 REMARK 500 2 ARG A 410 -115.87 -74.65 REMARK 500 2 LEU A 411 30.66 -86.20 REMARK 500 2 THR A 442 -141.21 -82.45 REMARK 500 2 TYR A 443 28.99 -71.92 REMARK 500 2 PRO A 448 65.91 -66.29 REMARK 500 2 SER A 452 161.84 71.01 REMARK 500 2 PRO A 453 93.34 -56.67 REMARK 500 3 ARG A 335 50.67 -147.31 REMARK 500 3 ARG A 410 -99.61 -75.94 REMARK 500 3 GLN A 441 -159.85 -92.86 REMARK 500 3 THR A 442 -177.96 -60.90 REMARK 500 3 PRO A 448 107.61 -53.97 REMARK 500 3 PRO A 453 88.51 -54.42 REMARK 500 4 ARG A 335 55.56 -166.31 REMARK 500 4 THR A 383 -68.19 -105.78 REMARK 500 4 ARG A 410 -100.51 -55.44 REMARK 500 4 GLN A 441 -161.08 -108.95 REMARK 500 4 THR A 442 179.22 -57.22 REMARK 500 4 TYR A 443 41.13 -79.72 REMARK 500 4 PRO A 448 101.27 -55.85 REMARK 500 4 VAL A 454 94.13 -67.57 REMARK 500 5 ARG A 335 53.35 -162.82 REMARK 500 5 THR A 383 -90.67 -93.13 REMARK 500 5 ASN A 384 45.16 -86.62 REMARK 500 5 ARG A 410 -86.09 -63.59 REMARK 500 5 GLU A 445 105.35 -47.94 REMARK 500 5 PRO A 448 71.02 -60.45 REMARK 500 5 THR A 449 178.61 52.64 REMARK 500 5 PRO A 453 74.69 -59.40 REMARK 500 6 MET A 334 -83.12 -61.45 REMARK 500 6 THR A 383 -82.27 -113.50 REMARK 500 6 ARG A 410 -105.28 -67.80 REMARK 500 6 LEU A 411 30.69 -89.59 REMARK 500 6 MET A 423 2.55 -69.94 REMARK 500 6 THR A 442 -94.94 -70.17 REMARK 500 6 PRO A 448 84.31 -57.45 REMARK 500 6 PRO A 453 105.80 -49.93 REMARK 500 6 VAL A 454 -69.96 -131.28 REMARK 500 7 HIS A 333 177.19 64.57 REMARK 500 7 LEU A 336 -179.31 68.29 REMARK 500 REMARK 500 THIS ENTRY HAS 166 RAMACHANDRAN OUTLIERS. 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 19 ARG A 349 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17742 RELATED DB: BMRB REMARK 900 RELATED ID: 2LF7 RELATED DB: PDB DBREF 2LF8 A 335 458 UNP P97360 ETV6_MOUSE 335 458 SEQADV 2LF8 GLY A 331 UNP P97360 EXPRESSION TAG SEQADV 2LF8 SER A 332 UNP P97360 EXPRESSION TAG SEQADV 2LF8 HIS A 333 UNP P97360 EXPRESSION TAG SEQADV 2LF8 MET A 334 UNP P97360 EXPRESSION TAG SEQRES 1 A 128 GLY SER HIS MET ARG LEU LEU TRP ASP TYR VAL TYR GLN SEQRES 2 A 128 LEU LEU SER ASP SER ARG TYR GLU ASN PHE ILE ARG TRP SEQRES 3 A 128 GLU ASP LYS GLU SER LYS ILE PHE ARG ILE VAL ASP PRO SEQRES 4 A 128 ASN GLY LEU ALA ARG LEU TRP GLY ASN HIS LYS ASN ARG SEQRES 5 A 128 THR ASN MET THR TYR GLU LYS MET SER ARG ALA LEU ARG SEQRES 6 A 128 HIS TYR TYR LYS LEU ASN ILE ILE ARG LYS GLU PRO GLY SEQRES 7 A 128 GLN ARG LEU LEU PHE ARG PHE MET LYS THR PRO ASP GLU SEQRES 8 A 128 ILE MET SER GLY ARG THR ASP ARG LEU GLU HIS LEU GLU SEQRES 9 A 128 SER GLN VAL LEU ASP GLU GLN THR TYR GLN GLU ASP GLU SEQRES 10 A 128 PRO THR ILE ALA SER PRO VAL GLY TRP PRO ARG HELIX 1 1 LEU A 336 LEU A 345 1 10 HELIX 2 2 SER A 346 ASN A 352 5 7 HELIX 3 3 ASP A 368 LYS A 380 1 13 HELIX 4 4 THR A 386 LEU A 400 1 15 HELIX 5 5 THR A 418 MET A 423 1 6 HELIX 6 6 ARG A 426 GLN A 441 1 16 SHEET 1 A 4 ILE A 354 ASP A 358 0 SHEET 2 A 4 ILE A 363 ILE A 366 -1 O ARG A 365 N ARG A 355 SHEET 3 A 4 LEU A 412 PHE A 415 -1 O PHE A 413 N PHE A 364 SHEET 4 A 4 ILE A 403 LYS A 405 -1 N ARG A 404 O ARG A 414 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