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- PDB-7d0q: Crystal structure of human HBO1-BRPF2 in complex with butyryl-coe... -

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Basic information

Entry
Database: PDB / ID: 7d0q
TitleCrystal structure of human HBO1-BRPF2 in complex with butyryl-coenzyme A
Components
  • BRD1 protein
  • Histone acetyltransferase KAT7
KeywordsTRANSFERASE / histone acetyltransferase / complex / HBO1 / BRPF2 / butyryl-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 / positive regulation of hematopoietic stem cell proliferation / regulation of DNA biosynthetic process / 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 / 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 / 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 / regulation of DNA replication / site of DNA damage / DNA replication origin binding / 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 / 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
Butyryl Coenzyme A / Histone acetyltransferase KAT7 / BRD1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 1.4Nov 20, 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

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)39,2976
Polymers38,2962
Non-polymers1,0014
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-19 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.871, 39.599, 87.900
Angle α, β, γ (deg.)90.000, 122.890, 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 , 5 types, 58 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BCO / Butyryl Coenzyme A / S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} butanethioate (non-preferred name)


Mass: 837.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H42N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, pH 8.5, 20% w/v PEG 6000

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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: 2.2→50.01 Å / Num. obs: 18377 / % possible obs: 99.3 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 28.6
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1836 / 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: 2.21→50.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 18.039 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 925 5 %RANDOM
Rwork0.186 ---
obs0.1889 17452 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.83 Å2 / Biso mean: 69.279 Å2 / Biso min: 33.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å20 Å2-0.9 Å2
2--2.39 Å20 Å2
3---0.89 Å2
Refinement stepCycle: final / Resolution: 2.21→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 59 54 2593
Biso mean--74.02 67.24 -
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192598
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9993512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.86723.86114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59815462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8881513
X-RAY DIFFRACTIONr_chiral_restr0.0590.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211918
X-RAY DIFFRACTIONr_rigid_bond_restr7.76832598
X-RAY DIFFRACTIONr_sphericity_free35.277518
X-RAY DIFFRACTIONr_sphericity_bonded37.88152575
LS refinement shellResolution: 2.211→2.268 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 62 -
Rwork0.259 1079 -
all-1141 -
obs--84.77 %
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)
10.00810.00350.02420.00170.01030.07340.00070.00250.00240.0013-0.00160.00330.00220.00710.00080.0047-0.00330.0150.0729-0.00270.0493199.4092-7.274992.1558
20.6992-0.5180.92410.501-0.41361.8482-0.14820.08670.05410.0807-0.02420.002-0.2680.20320.17240.0535-0.0185-0.04290.05130.02420.0654170.539-8.0139104.0897
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A336 - 611
2X-RAY DIFFRACTION2B37 - 64

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