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- PDB-2wp2: Structure of Brdt bromodomain BD1 bound to a diacetylated histone... -

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Basic information

Entry
Database: PDB / ID: 2wp2
TitleStructure of Brdt bromodomain BD1 bound to a diacetylated histone H4 peptide.
Components
  • BROMODOMAIN TESTIS-SPECIFIC PROTEIN
  • HISTONE H4
KeywordsTRANSCRIPTION/PEPTIDE / TRANSCRIPTION-PEPTIDE COMPLEX / TRANSCRIPTION REGULATION / BRDT / ACETYLLYSINE / NUCLEUS / COILED COIL / CHROMOSOMAL PROTEIN / NUCLEOSOME
Function / homology
Function and homology information


Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / Recognition and association of DNA glycosylase with site containing an affected purine ...Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / HDACs deacetylate histones / PRC2 methylates histones and DNA / Processing of DNA double-strand break ends / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / sperm DNA condensation / RMTs methylate histone arginines / male meiotic nuclear division / Estrogen-dependent gene expression / regulation of RNA splicing / male meiosis I / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / RNA splicing / histone reader activity / : / mRNA processing / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / spermatogenesis / histone binding / chromatin remodeling / protein heterodimerization activity / positive regulation of gene expression / regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / TATA box binding protein associated factor ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 / Bromodomain, conserved site / Bromodomain signature. / Histone-fold / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H4 / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 / 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 1.3May 1, 2024Group: 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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 H4
Q: HISTONE H4


Theoretical massNumber of molelcules
Total (without water)32,7104
Polymers32,7104
Non-polymers00
Water2,000111
1
A: BROMODOMAIN TESTIS-SPECIFIC PROTEIN
P: HISTONE H4


Theoretical massNumber of molelcules
Total (without water)16,3552
Polymers16,3552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-9.9 kcal/mol
Surface area7430 Å2
MethodPISA
2
B: BROMODOMAIN TESTIS-SPECIFIC PROTEIN
Q: HISTONE H4


Theoretical massNumber of molelcules
Total (without water)16,3552
Polymers16,3552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-8.1 kcal/mol
Surface area7450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.293, 61.224, 97.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.69995, 0.71181, -0.05824), (0.71122, -0.70215, -0.03401), (-0.0651, -0.01762, -0.99772)-1.42736, 1.42373, -23.26795
2given(0.69995, 0.71181, -0.05824), (0.71122, -0.70215, -0.03401), (-0.0651, -0.01762, -0.99772)-1.42736, 1.42373, -23.26795

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Components

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


Mass: 14271.539 Da / Num. of mol.: 2 / Fragment: BROMODOMAIN 1, RESIDUES 17-136
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 H4


Mass: 2083.428 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-21 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P62806
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.2 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 15 MG/ML BRDT-BD1 PROTEIN WAS MIXED WITH H4-ACK5/K8 PEPTIDE IN A 1:20 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD FROM 2.4 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.37→44 Å / Num. obs: 12142 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.1
Reflection shellResolution: 2.37→2.4 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.3 / % possible all: 63.3

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BROMODOMAIN BD2 FROM BRDT

Resolution: 2.37→44 Å / Rfactor Rfree error: 0.011 / 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 BECAUSE OF POOR DENSITY - CHAIN A RESIDUES 21-26, CHAIN B RESIDUES 18-26, CHAIN P RESIDUES 1-3 AND 13-20, CHAIN Q RESIDUES 1 AND 13-20. THE FOLLOWING ...Details: THE FOLLOWING RESIDUES WERE NOT MODELLED BECAUSE OF POOR DENSITY - CHAIN A RESIDUES 21-26, CHAIN B RESIDUES 18-26, CHAIN P RESIDUES 1-3 AND 13-20, CHAIN Q RESIDUES 1 AND 13-20. THE FOLLOWING RESIDUES WERE MODELLED AS ALANINE - CHAIN A RESIDUES 18-21, CHAIN P RESIDUE 12, AND CHAIN Q RESIDUE 12. FOLLOWING RESIDUES WERE MODELLED AS ALA: A18-21, P12, Q12.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 587 4.8 %RANDOM
Rwork0.217 ---
obs0.217 12142 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.9719 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.861 Å20 Å20 Å2
2---0.794 Å20 Å2
3---1.655 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati sigma a0.27 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.37→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 0 111 2099
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00624
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_deg1.154
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
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: 2.37→2.52 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 86 4.9 %
Rwork0.278 1682 -
obs--86.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP_ALY.PARAM

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