PDB Short entry for 2L5E HEADER NUCLEAR PROTEIN/TRANSCRIPTION 31-OCT-10 2L5E TITLE COMPLEX BETWEEN BD1 OF BRD3 AND GATA-1 C-TAIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BROMODOMAIN CONTAINING 3, ISOFORM CRA_D; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GATA-1; COMPND 8 CHAIN: B; COMPND 9 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: BRD3, MCG_11349, RP23-328F3.1-001; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX6P; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. KEYWDS GATA-1, BRD3, HISTONE CODE, NUCLEAR PROTEIN-TRANSCRIPTION COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.GAMSJAEGER,S.R.WEBB,J.M.LAMONICA,G.A.BLOBEL,J.P.MACKAY REVDAT 3 26-FEB-20 2L5E 1 REMARK SEQADV LINK REVDAT 2 26-JUL-17 2L5E 1 JRNL REVDAT 1 18-MAY-11 2L5E 0 JRNL AUTH R.GAMSJAEGER,S.R.WEBB,J.M.LAMONICA,A.BILLIN,G.A.BLOBEL, JRNL AUTH 2 J.P.MACKAY JRNL TITL STRUCTURAL BASIS AND SPECIFICITY OF ACETYLATED TRANSCRIPTION JRNL TITL 2 FACTOR GATA1 RECOGNITION BY BET FAMILY BROMODOMAIN PROTEIN JRNL TITL 3 BRD3. JRNL REF MOL. CELL. BIOL. V. 31 2632 2011 JRNL REFN ESSN 1098-5549 JRNL PMID 21555453 JRNL DOI 10.1128/MCB.05413-11 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE REMARK 3 -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON, REMARK 3 WARREN (CNS), BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CNS/ARIA1.2 REMARK 4 REMARK 4 2L5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000101978. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-1.5 MM [U-13C; U-15N] REMARK 210 ENTITY_1-1, 0.5-1.5 MM ENTITY_2- REMARK 210 2, 100 MM NACL-3, 20 MM TRIS-4, REMARK 210 1 MM DTT-5, 90% H2O/10% D2O; 0.5- REMARK 210 1.5 MM [U-13C; U-15N] ENTITY_1-6, REMARK 210 0.5-1.5 MM ENTITY_2-7, 100 MM REMARK 210 NACL-8, 20 MM TRIS-9, 1 MM DTT- REMARK 210 10, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HNCO; 3D HN(CO)CA; 3D HBHA(CO)NH; REMARK 210 3D HCCH-TOCSY; 3D HNHA; 3D REMARK 210 HCC(CO)NH TOCSY; 3D CC(CO)NH REMARK 210 TOCSY; 3D 13C SEP (F2) 15N13C REMARK 210 FILTERED (F1) NOESY; 3D 13C SEP REMARK 210 (F1) 15N13C FILTERED (F3) NOESY; REMARK 210 2D 15N13C FILTERED NOESY; 2D REMARK 210 15N13C FILTERED TOCSY; 3D 13C REMARK 210 NOESY; 3D 15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 20 REMARK 465 LYS B 308 REMARK 465 ALA B 309 REMARK 465 SER B 310 REMARK 465 ARG B 317 REMARK 465 GLY B 318 REMARK 465 SER B 319 REMARK 465 ASN B 320 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 3 TYR A 60 CE1 TYR A 60 CZ 0.095 REMARK 500 3 TYR A 60 CZ TYR A 60 CE2 -0.099 REMARK 500 4 TYR A 60 CE1 TYR A 60 CZ 0.083 REMARK 500 4 TYR A 60 CZ TYR A 60 CE2 -0.089 REMARK 500 7 TYR A 95 CE1 TYR A 95 CZ 0.094 REMARK 500 7 TYR A 95 CZ TYR A 95 CE2 -0.081 REMARK 500 12 TYR A 95 CE1 TYR A 95 CZ 0.092 REMARK 500 12 TYR A 95 CZ TYR A 95 CE2 -0.100 REMARK 500 13 TYR A 60 CE1 TYR A 60 CZ 0.081 REMARK 500 13 TYR A 60 CZ TYR A 60 CE2 -0.087 REMARK 500 16 TYR A 60 CZ TYR A 60 CE2 -0.083 REMARK 500 18 TYR A 60 CE1 TYR A 60 CZ 0.080 REMARK 500 18 TYR A 60 CZ TYR A 60 CE2 -0.087 REMARK 500 19 TYR A 60 CZ TYR A 60 CE2 -0.082 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 ALA A 65 -45.26 76.18 REMARK 500 1 PRO A 80 91.97 -60.99 REMARK 500 1 ASP A 82 -116.71 -143.05 REMARK 500 1 GLU A 144 135.37 74.28 REMARK 500 1 LYS B 314 84.02 61.55 REMARK 500 2 PHE A 59 45.81 -109.15 REMARK 500 2 ALA A 65 -88.29 55.68 REMARK 500 2 PRO A 80 93.44 -67.19 REMARK 500 2 ASP A 82 -142.15 -151.06 REMARK 500 2 GLN A 142 21.39 -76.08 REMARK 500 2 GLU A 144 113.03 75.18 REMARK 500 2 ALY B 312 76.20 -102.73 REMARK 500 2 ALY B 315 -93.03 -103.62 REMARK 500 3 LEU A 22 42.91 -101.98 REMARK 500 3 SER A 24 176.77 58.55 REMARK 500 3 ALA A 65 -21.62 86.05 REMARK 500 3 ASN A 69 71.78 56.29 REMARK 500 3 ASP A 82 -129.21 -133.61 REMARK 500 3 GLU A 144 65.70 60.55 REMARK 500 4 ALA A 65 -32.27 80.37 REMARK 500 4 ASP A 82 -134.81 -153.98 REMARK 500 4 GLU A 144 98.55 67.82 REMARK 500 5 SER A 27 116.40 -173.66 REMARK 500 5 ARG A 34 -117.09 -73.92 REMARK 500 5 LYS A 35 129.04 -175.06 REMARK 500 5 ALA A 65 -21.31 85.72 REMARK 500 5 PRO A 80 93.63 -65.95 REMARK 500 5 ASP A 82 -121.72 -139.65 REMARK 500 5 GLN A 142 29.45 -75.78 REMARK 500 5 GLU A 144 73.27 63.27 REMARK 500 6 SER A 27 138.78 -177.11 REMARK 500 6 ALA A 65 -55.73 77.31 REMARK 500 6 PRO A 80 87.11 -69.11 REMARK 500 6 ASP A 82 -144.64 -143.18 REMARK 500 6 ASN A 93 72.04 58.25 REMARK 500 6 GLU A 144 93.26 67.68 REMARK 500 7 ALA A 65 -40.43 74.95 REMARK 500 7 PRO A 80 89.95 -68.34 REMARK 500 7 ASP A 82 -115.39 -151.67 REMARK 500 7 TYR A 95 -145.15 -80.71 REMARK 500 7 TRP A 96 -53.59 -126.83 REMARK 500 7 GLU A 143 -111.52 -100.22 REMARK 500 7 GLU A 144 131.35 178.30 REMARK 500 7 ALY B 315 -167.63 -120.60 REMARK 500 8 LEU A 70 70.09 -119.81 REMARK 500 8 PRO A 80 92.87 -68.59 REMARK 500 8 ASP A 82 -123.19 -151.49 REMARK 500 8 GLU A 144 143.17 74.72 REMARK 500 9 ALA A 65 -17.55 77.93 REMARK 500 9 ASP A 82 -116.21 -136.99 REMARK 500 REMARK 500 THIS ENTRY HAS 118 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 7 TYR A 94 0.05 SIDE CHAIN REMARK 500 7 TYR A 95 0.07 SIDE CHAIN REMARK 500 8 TYR A 95 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17270 RELATED DB: BMRB DBREF 2L5E A 25 147 UNP Q3TUI3 Q3TUI3_MOUSE 25 147 DBREF 2L5E B 308 320 PDB 2L5E 2L5E 308 320 SEQADV 2L5E GLY A 20 UNP Q3TUI3 EXPRESSION TAG SEQADV 2L5E PRO A 21 UNP Q3TUI3 EXPRESSION TAG SEQADV 2L5E LEU A 22 UNP Q3TUI3 EXPRESSION TAG SEQADV 2L5E GLY A 23 UNP Q3TUI3 EXPRESSION TAG SEQADV 2L5E SER A 24 UNP Q3TUI3 EXPRESSION TAG SEQRES 1 A 128 GLY PRO LEU GLY SER GLU VAL SER ASN PRO SER LYS PRO SEQRES 2 A 128 GLY ARG LYS THR ASN GLN LEU GLN TYR MET GLN ASN VAL SEQRES 3 A 128 VAL VAL LYS THR LEU TRP LYS HIS GLN PHE ALA TRP PRO SEQRES 4 A 128 PHE TYR GLN PRO VAL ASP ALA ILE LYS LEU ASN LEU PRO SEQRES 5 A 128 ASP TYR HIS LYS ILE ILE LYS ASN PRO MET ASP MET GLY SEQRES 6 A 128 THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP SER SEQRES 7 A 128 ALA SER GLU CYS MET GLN ASP PHE ASN THR MET PHE THR SEQRES 8 A 128 ASN CYS TYR ILE TYR ASN LYS PRO THR ASP ASP ILE VAL SEQRES 9 A 128 LEU MET ALA GLN ALA LEU GLU LYS ILE PHE LEU GLN LYS SEQRES 10 A 128 VAL ALA GLN MET PRO GLN GLU GLU VAL GLU LEU SEQRES 1 B 13 LYS ALA SER GLY ALY GLY LYS ALY LYS ARG GLY SER ASN MODRES 2L5E ALY B 312 LYS N(6)-ACETYLLYSINE MODRES 2L5E ALY B 315 LYS N(6)-ACETYLLYSINE HET ALY B 312 26 HET ALY B 315 26 HETNAM ALY N(6)-ACETYLLYSINE FORMUL 2 ALY 2(C8 H16 N2 O3) HELIX 1 1 THR A 36 VAL A 45 1 10 HELIX 2 2 VAL A 45 LYS A 52 1 8 HELIX 3 3 ALA A 56 TYR A 60 5 5 HELIX 4 4 ASP A 72 ILE A 77 1 6 HELIX 5 5 MET A 83 ASN A 92 1 10 HELIX 6 6 SER A 97 SER A 99 5 3 HELIX 7 7 GLU A 100 ASN A 116 1 17 HELIX 8 8 ASP A 120 ALA A 138 1 19 LINK C GLY B 311 N ALY B 312 1555 1555 1.33 LINK C ALY B 312 N GLY B 313 1555 1555 1.32 LINK C LYS B 314 N ALY B 315 1555 1555 1.33 LINK C ALY B 315 N LYS B 316 1555 1555 1.32 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