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- PDB-2e3k: Crystal structure of the human Brd2 second bromodomain in complex... -

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Basic information

Entry
Database: PDB / ID: 2e3k
TitleCrystal structure of the human Brd2 second bromodomain in complexed with the acetylated histone H4 peptide
Components
  • 15-mer peptide from Histone H4
  • Bromodomain-containing protein 2BRD2
KeywordsTRANSCRIPTION / Bromodomain / Binds to acetylated histone tails / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / chromatin looping / acetylation-dependent protein binding / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I ...HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / chromatin looping / acetylation-dependent protein binding / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / spermatogenesis / nuclear speck / protein heterodimerization activity / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Bromodomain-like / Histone Acetyltransferase; Chain A / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H4 / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPadmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structural basis for diacetylated histone H4 tail recognition by the second bromodomain of human BRD2
Authors: Padmanabhan, B. / Umehara, T. / Nakano, K. / Jang, M.K. / Ozato, K. / Yokohama, S.
History
DepositionNov 27, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
D: Bromodomain-containing protein 2
Q: 15-mer peptide from Histone H4
R: 15-mer peptide from Histone H4


Theoretical massNumber of molelcules
Total (without water)55,4826
Polymers55,4826
Non-polymers00
Water7,422412
1
A: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
Q: 15-mer peptide from Histone H4


Theoretical massNumber of molelcules
Total (without water)27,7413
Polymers27,7413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 2
D: Bromodomain-containing protein 2
R: 15-mer peptide from Histone H4


Theoretical massNumber of molelcules
Total (without water)27,7413
Polymers27,7413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.828, 128.591, 45.847
Angle α, β, γ (deg.)90.00, 104.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 5 / Auth seq-ID: 350 - 455 / Label seq-ID: 7 - 112

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
12BB
22DD

NCS ensembles :
ID
1
2

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Components

#1: Protein
Bromodomain-containing protein 2 / BRD2 / Protein RING3 / O27.1.1


Mass: 13184.141 Da / Num. of mol.: 4 / Fragment: The second bromodomain, BD2, residues 348-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Protein/peptide 15-mer peptide from Histone H4


Mass: 1372.534 Da / Num. of mol.: 2 / Fragment: N-terminal H4 di-acetylated tail / Source method: obtained synthetically
Details: Synthetic peptide. The sequence of the peptide is naturally found in other source organism in addition to Baker's yeast refered in DBREF record.
References: UniProt: P02309
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG4000, Ammonium Acetate,, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 22955 / Num. obs: 22434 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.048
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.166 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVV

2dvv


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.036 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.459 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26757 1144 5.1 %RANDOM
Rwork0.20096 ---
obs0.20447 21151 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.691 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å21.26 Å2
2---0.85 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 0 412 4178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0213864
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.9585189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.945457
X-RAY DIFFRACTIONr_chiral_restr0.120.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022969
X-RAY DIFFRACTIONr_nbd_refined0.2460.22035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.225
X-RAY DIFFRACTIONr_mcbond_it1.48922316
X-RAY DIFFRACTIONr_mcangle_it2.42433681
X-RAY DIFFRACTIONr_scbond_it2.75331548
X-RAY DIFFRACTIONr_scangle_it3.72841508
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A424medium positional0.290.5
2B424medium positional0.350.5
1A452loose positional0.725
2B452loose positional0.895
1A424medium thermal1.752
2B424medium thermal1.882
1A452loose thermal2.9210
2B452loose thermal2.6310
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.3 75
Rwork0.188 1548
obs-1548

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