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- PDB-7d0r: Crystal structure of human HBO1-BRPF2 in complex with crotonoyl-c... -

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Basic information

Entry
Database: PDB / ID: 7d0r
TitleCrystal structure of human HBO1-BRPF2 in complex with crotonoyl-coenzyme A
Components
  • BRD1 protein
  • Histone acetyltransferase KAT7
KeywordsTRANSFERASE / histone acetyltransferase / complex / HBO1 / BRPF2 / crotonoyl-CoA / acylation
Function / homology
Function and homology information


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 / natural killer cell differentiation / internal peptidyl-lysine acetylation ...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 / natural killer cell differentiation / internal peptidyl-lysine acetylation / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / regulation of nucleotide-excision repair / stress-activated protein kinase signaling cascade / histone H3-K14 acetyltransferase complex / positive regulation of DNA-templated transcription, elongation / regulation of DNA-templated DNA replication initiation / histone acetyltransferase activity / regulation of DNA replication / site of DNA damage / DNA replication origin binding / chromosome, centromeric region / histone acetyltransferase complex / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / positive regulation of DNA replication / transcription coregulator activity / regulation of cell growth / positive regulation of protein localization to nucleus / HATs acetylate histones / chromosome / DNA replication / regulation of cell cycle / DNA repair / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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 / 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
CROTONYL COENZYME A / Histone acetyltransferase KAT7 / BRD1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,2595
Polymers38,2962
Non-polymers9633
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-15 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.345, 39.636, 88.096
Angle α, β, γ (deg.)90.000, 123.240, 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, 92 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-COO / CROTONYL COENZYME A


Mass: 835.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.03 M Citric acid, 0.07 M BIS-TRIS propane, pH 7.6, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50.01 Å / Num. obs: 26858 / % possible obs: 97.8 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 38.5
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2647 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GK9

5gk9


Resolution: 1.95→50.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.966 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.419 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1361 5.1 %RANDOM
Rwork0.1824 ---
obs0.1848 25279 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.31 Å2 / Biso mean: 53.543 Å2 / Biso min: 21.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å2-0 Å2-0.28 Å2
2--2.75 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: final / Resolution: 1.95→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 58 89 2581
Biso mean--60 52.25 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192562
X-RAY DIFFRACTIONr_bond_other_d0.0020.022425
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9993466
X-RAY DIFFRACTIONr_angle_other_deg1.30135590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54323.611108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61415451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8781513
X-RAY DIFFRACTIONr_chiral_restr0.320.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212790
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02578
X-RAY DIFFRACTIONr_rigid_bond_restr3.98632562
X-RAY DIFFRACTIONr_sphericity_free30.123545
X-RAY DIFFRACTIONr_sphericity_bonded32.27452546
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 99 -
Rwork0.267 1829 -
all-1928 -
obs--97.52 %

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