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- PDB-5gk9: Crystal structure of human HBO1 in complex with BRPF2 -

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Basic information

Entry
Database: PDB / ID: 5gk9
TitleCrystal structure of human HBO1 in complex with BRPF2
Components
  • BRD1 protein
  • Histone acetyltransferase KAT7
KeywordsTRANSFERASE/METAL BINDING PROTEIN / HAT / TRANSFERASE-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


histone H3K4 acetyltransferase activity / response to hydroxyurea / response to actinomycin D / response to dithiothreitol / response to anisomycin / DNA replication-dependent chromatin disassembly / response to sorbitol / positive regulation of hematopoietic stem cell proliferation / regulation of DNA biosynthetic process / histone H3K23 acetyltransferase activity ...histone H3K4 acetyltransferase activity / response to hydroxyurea / response to actinomycin D / response to dithiothreitol / response to anisomycin / DNA replication-dependent chromatin disassembly / response to sorbitol / positive regulation of hematopoietic stem cell proliferation / regulation of DNA biosynthetic process / histone H3K23 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / natural killer cell differentiation / histone H4 acetyltransferase activity / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / regulation of nucleotide-excision repair / stress-activated protein kinase signaling cascade / regulation of DNA-templated DNA replication initiation / positive regulation of DNA-templated transcription, elongation / histone H3-K14 acetyltransferase complex / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / erythrocyte maturation / regulation of DNA replication / DNA replication origin binding / site of DNA damage / response to immobilization stress / chromosome, centromeric region / histone acetyltransferase complex / response to electrical stimulus / histone acetyltransferase activity / histone acetyltransferase / Regulation of TP53 Activity through Acetylation / positive regulation of erythrocyte differentiation / histone reader activity / transcription initiation-coupled chromatin remodeling / positive regulation of DNA replication / regulation of cell growth / transcription coregulator activity / positive regulation of protein localization to nucleus / chromosome / HATs acetylate histones / histone binding / perikaryon / DNA replication / regulation of cell cycle / nuclear speck / chromatin remodeling / DNA repair / chromatin binding / dendrite / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / : / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. ...Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / : / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / BRPF2, ePHD domain / BRPF2, PHD domain / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / Histone acetyltransferase KAT7 / Bromodomain-containing protein 1 / BRD1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTao, Y. / Zhu, J. / Xu, S. / Ding, J.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural and mechanistic insights into regulation of HBO1 histone acetyltransferase activity by BRPF2.
Authors: Tao, Y. / Zhong, C. / Zhu, J. / Xu, S. / Ding, J.
History
DepositionJul 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase KAT7
B: BRD1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1304
Polymers38,2552
Non-polymers8752
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-21 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.470, 39.321, 87.666
Angle α, β, γ (deg.)90.000, 122.100, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-815-

HOH

21B-104-

HOH

31B-105-

HOH

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Components

#1: Protein Histone acetyltransferase KAT7 / Histone acetyltransferase binding to ORC1 / Lysine acetyltransferase 7 / MOZ / YBF2/SAS3 / SAS2 and ...Histone acetyltransferase binding to ORC1 / Lysine acetyltransferase 7 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 2 / MYST-2


Mass: 32555.945 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 336-611
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT7, HBO1, HBOa, MYST2 / Production host: Escherichia coli (E. coli) / References: UniProt: O95251, histone acetyltransferase
#2: Protein/peptide BRD1 protein


Mass: 5699.317 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 31-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD1
Production host: Escherichia coli BL21-Gold(DE3)pLysS AG (bacteria)
References: UniProt: Q86X06, UniProt: O95696*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: Tacsimate Tris-HCl, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 0.9786 Å
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 14322 / % possible obs: 97.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 18
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3.6 / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.2data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GIV

2giv


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.036 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.421 / ESU R Free: 0.273 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 729 5.1 %RANDOM
Rwork0.233 ---
obs0.26 13593 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.28 Å2 / Biso mean: 49.289 Å2 / Biso min: 22.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å2-0 Å2-0.28 Å2
2--3.84 Å20 Å2
3----0.62 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 52 25 2480
Biso mean--40.13 37.63 -
Num. residues----289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022517
X-RAY DIFFRACTIONr_bond_other_d0.0060.022406
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9943402
X-RAY DIFFRACTIONr_angle_other_deg0.9543.0065559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4925286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7623.604111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.34715465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8611513
X-RAY DIFFRACTIONr_chiral_restr0.2340.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
LS refinement shellResolution: 2.399→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 49 -
Rwork0.273 1000 -
all-1049 -
obs--94.85 %

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