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- PDB-2wp1: Structure of Brdt bromodomain 2 bound to an acetylated histone H3... -

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Basic information

Entry
Database: PDB / ID: 2wp1
TitleStructure of Brdt bromodomain 2 bound to an acetylated histone H3 peptide
Components
  • BROMODOMAIN TESTIS-SPECIFIC PROTEIN
  • HISTONE H3
KeywordsTRANSCRIPTION/PEPTIDE / TRANSCRIPTION PEPTIDE COMPLEX / TRANSCRIPTION REGULATION / ACETYLLYSINE BRDT / NUCLEUS / COILED COIL / CHROMOSOMAL PROTEIN / NUCLEOSOME / TRANSCRIPTION-PEPTIDE complex
Function / homology
Function and homology information


Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / sperm DNA condensation / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / male meiotic nuclear division ...Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / sperm DNA condensation / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / male meiotic nuclear division / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / regulation of RNA splicing / male meiosis I / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / spermatogenesis / chromatin remodeling / protein heterodimerization activity / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / protein-containing complex / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H3 signature 1. / Histone H3 signature 2. ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Bromodomain-like / Histone Acetyltransferase; Chain A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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 H3 / Histone H3.1 / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMoriniere, J. / Rousseaux, S. / Steuerwald, U. / Soler-Lopez, M. / Curtet, S. / Vitte, A.-L. / Govin, J. / Gaucher, J. / Sadoul, K. / Hart, D.J. ...Moriniere, J. / Rousseaux, S. / Steuerwald, U. / Soler-Lopez, M. / Curtet, S. / Vitte, A.-L. / Govin, J. / Gaucher, J. / Sadoul, K. / Hart, D.J. / Krijgsveld, J. / Khochbin, S. / Mueller, C.W. / Petosa, C.
CitationJournal: Nature / Year: 2009
Title: Cooperative Binding of Two Acetylation Marks on a Histone Tail by a Single Bromodomain.
Authors: Moriniere, J. / Rousseaux, S. / Steuerwald, U. / Soler-Lopez, M. / Curtet, S. / Vitte, A.-L. / Govin, J. / Gaucher, J. / Sadoul, K. / Hart, D.J. / Krijgsveld, J. / Khochbin, S. / Mueller, C.W. / Petosa, C.
History
DepositionAug 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BROMODOMAIN TESTIS-SPECIFIC PROTEIN
B: BROMODOMAIN TESTIS-SPECIFIC PROTEIN
P: HISTONE H3
Q: HISTONE H3


Theoretical massNumber of molelcules
Total (without water)31,8794
Polymers31,8794
Non-polymers00
Water3,801211
1
A: BROMODOMAIN TESTIS-SPECIFIC PROTEIN
P: HISTONE H3


Theoretical massNumber of molelcules
Total (without water)15,9392
Polymers15,9392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-7.4 kcal/mol
Surface area7990 Å2
MethodPISA
2
B: BROMODOMAIN TESTIS-SPECIFIC PROTEIN
Q: HISTONE H3


Theoretical massNumber of molelcules
Total (without water)15,9392
Polymers15,9392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8.2 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.300, 101.300, 79.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-2012-

HOH

21B-2019-

HOH

31B-2068-

HOH

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Components

#1: Protein BROMODOMAIN TESTIS-SPECIFIC PROTEIN / RING3-LIKE PROTEIN / BROMODOMAIN-CONTAINING FEMALE STERILE HOMEOTIC-LIKE PROTEIN


Mass: 14753.943 Da / Num. of mol.: 2 / Fragment: BROMODOMAIN 2, RESIDUES 257-382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q91Y44
#2: Protein/peptide HISTONE H3 /


Mass: 1185.438 Da / Num. of mol.: 2 / Fragment: ACETYLATED H3 PEPTIDE, RESIDUES 15-24 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: B9EI85, UniProt: P68433*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 3.23 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: BRDT BD2 PROTEIN AT 25 MG/ML WAS MIXED WITH H3-ACK18 PEPTIDE IN A 1:5 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 2.0 M AMMONIUM SULFATE, 2% PEG 400, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225
DetectorType: ADSC CCD / Detector: CCD / Date: May 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07225 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 22542 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 60.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.9 / % possible all: 93.9

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E6I

1e6i


Resolution: 2.1→40 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE FOLLOWING RESIDUES WERE NOT MODELLED DUE TO POOR DENSITY - CHAIN A RESIDUES 257-258 AND 382, CHAIN B RESIDUES 257-264 AND 377-382, CHAIN P RESIDUES 14 AND 22-23. THE FOLLOWING RESIDUES ...Details: THE FOLLOWING RESIDUES WERE NOT MODELLED DUE TO POOR DENSITY - CHAIN A RESIDUES 257-258 AND 382, CHAIN B RESIDUES 257-264 AND 377-382, CHAIN P RESIDUES 14 AND 22-23. THE FOLLOWING RESIDUES WERE MODELLED AS GLYCINE -CHAIN A RESIDUES 260-261 AND 381, CHAIN B RESIDUES 265-267, CHAIN Q RESIDUE 14.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1143 5.1 %RANDOM
Rwork0.234 ---
obs0.234 22542 91.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.97 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 72.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.052 Å20 Å20 Å2
2---0.052 Å20 Å2
3---0.104 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.34 Å
Luzzati sigma a0.37 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 0 211 2247
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007812
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.20706
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.458 166 4.4 %
Rwork0.464 3611 -
obs--94 %

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