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- PDB-7d0p: Crystal structure of human HBO1-BRPF2 in complex with propionyl-c... -

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Basic information

Entry
Database: PDB / ID: 7d0p
TitleCrystal structure of human HBO1-BRPF2 in complex with propionyl-coenzyme A
Components
  • BRD1 protein
  • Histone acetyltransferase KAT7
KeywordsTRANSFERASE / histone acetyltransferase / complex / HBO1 / BRPF2 / propionyl-CoA / acylation
Function / homology
Function and homology information


response to hydroxyurea / response to actinomycin D / response to dithiothreitol / response to anisomycin / histone H3K4 acetyltransferase activity / DNA replication-dependent chromatin disassembly / response to sorbitol / regulation of DNA biosynthetic process / positive regulation of hematopoietic stem cell proliferation / histone H3K23 acetyltransferase activity ...response to hydroxyurea / response to actinomycin D / response to dithiothreitol / response to anisomycin / histone H3K4 acetyltransferase activity / DNA replication-dependent chromatin disassembly / response to sorbitol / regulation of DNA biosynthetic process / positive regulation of hematopoietic stem cell proliferation / histone H3K23 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / natural killer cell differentiation / internal peptidyl-lysine acetylation / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / stress-activated protein kinase signaling cascade / regulation of nucleotide-excision repair / histone H3-K14 acetyltransferase complex / positive regulation of DNA-templated transcription, elongation / regulation of DNA-templated DNA replication initiation / MOZ/MORF histone acetyltransferase complex / regulation of DNA replication / DNA replication origin binding / site of DNA damage / histone acetyltransferase complex / T cell differentiation / chromosome, centromeric region / histone acetyltransferase activity / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / positive regulation of erythrocyte differentiation / positive regulation of DNA replication / transcription coregulator activity / regulation of cell growth / positive regulation of protein localization to nucleus / chromosome / HATs acetylate histones / chromatin organization / DNA replication / regulation of cell cycle / DNA repair / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
propionyl Coenzyme A / Histone acetyltransferase KAT7 / BRD1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, W. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800622 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: HBO1 is a versatile histone acyltransferase critical for promoter histone acylations.
Authors: Xiao, Y. / Li, W. / Yang, H. / Pan, L. / Zhang, L. / Lu, L. / Chen, J. / Wei, W. / Ye, J. / Li, J. / Li, G. / Zhang, Y. / Tan, M. / Ding, J. / Wong, J.
History
DepositionSep 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 29, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)39,2215
Polymers38,2962
Non-polymers9243
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-25 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.679, 39.306, 87.744
Angle α, β, γ (deg.)90.000, 123.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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: 32596.977 Da / Num. of mol.: 1
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 / BRPF2


Mass: 5699.317 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86X06

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Non-polymers , 4 types, 102 molecules

#3: Chemical ChemComp-1VU / propionyl Coenzyme A


Mass: 823.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 7.5, 12% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.8→50.01 Å / Num. obs: 33222 / % possible obs: 98 % / Redundancy: 6.5 % / CC1/2: 1 / Net I/av σ(I): 32.2 / Net I/σ(I): 0.05
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3140 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GK9

5gk9


Resolution: 1.8→50.01 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.929 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 1638 4.9 %RANDOM
Rwork0.1708 ---
obs0.1734 31519 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.26 Å2 / Biso mean: 49.202 Å2 / Biso min: 24.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å2-1.26 Å2
2--3.66 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 1.8→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 54 99 2579
Biso mean--41.12 50.14 -
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192538
X-RAY DIFFRACTIONr_bond_other_d0.0010.022369
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9963440
X-RAY DIFFRACTIONr_angle_other_deg2.80635458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7095302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42623.774106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20515433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5241512
X-RAY DIFFRACTIONr_chiral_restr0.0910.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212779
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02568
X-RAY DIFFRACTIONr_rigid_bond_restr5.65634907
X-RAY DIFFRACTIONr_sphericity_free32.122551
X-RAY DIFFRACTIONr_sphericity_bonded19.28354897
LS refinement shellResolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 108 -
Rwork0.319 2162 -
all-2270 -
obs--91.31 %

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