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- PDB-7d0o: Crystal structure of human HBO1-BRPF2 in apo form -

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Basic information

Entry
Database: PDB / ID: 7d0o
TitleCrystal structure of human HBO1-BRPF2 in apo form
Components
  • BRD1 protein
  • Histone acetyltransferase KAT7
KeywordsTRANSFERASE / histone acetyltransferase / complex / HBO1 / BRPF2
Function / homology
Function and homology information


histone H3K4 acetyltransferase activity / response to hydroxyurea / response to actinomycin D / response to dithiothreitol / response to anisomycin / response to sorbitol / positive regulation of hematopoietic stem cell proliferation / regulation of DNA biosynthetic process / histone H3K23 acetyltransferase activity / histone H4K5 acetyltransferase activity ...histone H3K4 acetyltransferase activity / response to hydroxyurea / response to actinomycin D / response to dithiothreitol / response to anisomycin / response to sorbitol / positive regulation of hematopoietic stem cell proliferation / regulation of DNA biosynthetic process / histone H3K23 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / DNA replication-dependent chromatin disassembly / histone H3K14 acetyltransferase activity / natural killer cell differentiation / histone H4 acetyltransferase activity / internal peptidyl-lysine acetylation / regulation of nucleotide-excision repair / positive regulation of DNA-templated transcription, elongation / histone H3-K14 acetyltransferase complex / regulation of DNA-templated DNA replication initiation / stress-activated protein kinase signaling cascade / DNA replication origin binding / site of DNA damage / regulation of DNA replication / chromosome, centromeric region / histone acetyltransferase complex / histone acetyltransferase activity / histone acetyltransferase / 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 / DNA replication / regulation of cell cycle / DNA repair / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / metal ion binding / 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. / BRPF2, ePHD domain ...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
Histone acetyltransferase KAT7 / BRD1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,4244
Polymers38,2962
Non-polymers1272
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-16 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.604, 38.372, 88.075
Angle α, β, γ (deg.)90.000, 122.600, 90.000
Int Tables number5
Space group name H-MC121

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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: 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.14 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: PSI PILATUS 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: 2.5→50.01 Å / Num. obs: 11980 / % possible obs: 95 % / Redundancy: 6.1 % / CC1/2: 0.97 / Net I/σ(I): 25.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 912 / CC1/2: 0.98 / % possible all: 73.8

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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: 2.51→50.01 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.845 / SU B: 29.739 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2901 415 4.9 %RANDOM
Rwork0.2457 ---
obs0.2478 8006 66.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.58 Å2 / Biso mean: 39.155 Å2 / Biso min: 9.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å2-0.72 Å2
2---0.38 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 2.51→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 5 35 2475
Biso mean--27.78 23.71 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192496
X-RAY DIFFRACTIONr_bond_other_d0.0030.022378
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9763368
X-RAY DIFFRACTIONr_angle_other_deg0.99835482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50323.704108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.97915450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2751513
X-RAY DIFFRACTIONr_chiral_restr0.0730.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212742
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02563
X-RAY DIFFRACTIONr_rigid_bond_restr1.58334874
X-RAY DIFFRACTIONr_sphericity_free31.212512
X-RAY DIFFRACTIONr_sphericity_bonded19.84654841
LS refinement shellResolution: 2.51→2.572 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.598 2 -
Rwork0.243 42 -
obs--4.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.63270.0753-0.05330.01430.00920.1195-0.0154-0.0327-0.0046-0.00960.0074-0.01720.0047-0.00790.0080.15480.00270.0010.18330.00150.1649201.3887-6.941292.5331
21.16971.2037-1.02051.2734-1.09680.96710.013-0.1576-0.02610.0225-0.04760.0041-0.0267-0.03010.03460.10620.05830.01180.398-0.00710.1179172.1975-7.2722104.5299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A336 - 608
2X-RAY DIFFRACTION2B38 - 65

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