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- PDB-7by1: Crystal structure of GCN5 PCAF N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 7by1
TitleCrystal structure of GCN5 PCAF N-terminal domain
ComponentsHistone acetyltransferase KAT2A
KeywordsUNKNOWN FUNCTION / Ubiquitin ligase
Function / homology
Function and homology information


metencephalon development / : / Formation of WDR5-containing histone-modifying complexes / histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / regulation of cartilage development / B-WICH complex positively regulates rRNA expression / regulation of bone development / fibroblast proliferation ...metencephalon development / : / Formation of WDR5-containing histone-modifying complexes / histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / regulation of cartilage development / B-WICH complex positively regulates rRNA expression / regulation of bone development / fibroblast proliferation / regulation of regulatory T cell differentiation / histone H4K12 acetyltransferase activity / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / Notch-HLH transcription pathway / histone H3K9 acetyltransferase activity / negative regulation of centriole replication / positive regulation of cell projection organization / oxoglutarate dehydrogenase complex / transcription factor TFTC complex / telencephalon development / somitogenesis / positive regulation of cardiac muscle cell differentiation / N-acetyltransferase activity / histone H3 acetyltransferase activity / regulation of T cell activation / Ub-specific processing proteases / histone H3K18 acetyltransferase activity / SAGA complex / ATAC complex / regulation of tubulin deacetylation / midbrain development / neural tube closure / multicellular organism growth / acetyltransferase activity / histone acetyltransferase activity / regulation of RNA splicing / regulation of stem cell population maintenance / intracellular distribution of mitochondria / histone acetyltransferase complex / limb development / negative regulation of gluconeogenesis / regulation of cell division / histone acetyltransferase / long-term memory / positive regulation of gluconeogenesis / gluconeogenesis / in utero embryonic development / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / regulation of DNA repair / regulation of embryonic development / positive regulation of cytokine production / protein modification process / cellular response to tumor necrosis factor / regulation of protein stability / cellular response to nerve growth factor stimulus / regulation of synaptic plasticity / response to nutrient levels / mitotic spindle / histone deacetylase binding / heart development / nervous system development / protein phosphatase binding / DNA-binding transcription factor binding / regulation of cell cycle / transcription coactivator activity / chromatin remodeling / centrosome / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain, conserved site / Bromodomain signature. ...PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Histone acetyltransferase KAT2A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsHibi, R. / Toma-Fukai, S. / Shimizu, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structure of GCN5 PCAF N-terminal domain reveals atypical ubiquitin ligase structure.
Authors: Toma-Fukai, S. / Hibi, R. / Naganuma, T. / Sakai, M. / Saijo, S. / Shimizu, N. / Matsumoto, M. / Shimizu, T.
History
DepositionApr 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT2A
B: Histone acetyltransferase KAT2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3666
Polymers73,1042
Non-polymers2624
Water7,476415
1
A: Histone acetyltransferase KAT2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6833
Polymers36,5521
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone acetyltransferase KAT2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6833
Polymers36,5521
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.069, 148.857, 58.998
Angle α, β, γ (deg.)90.00, 101.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 83 - 375 / Label seq-ID: 22 - 314

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Histone acetyltransferase KAT2A / General control of amino acid synthesis protein 5-like 2 / Histone acetyltransferase GCN5 / MmGCN5 ...General control of amino acid synthesis protein 5-like 2 / Histone acetyltransferase GCN5 / MmGCN5 / Histone glutaryltransferase KAT2A / Histone succinyltransferase KAT2A / Lysine acetyltransferase 2A


Mass: 36552.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kat2a, Gcn5l2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JHD2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM imidazole/MES (pH 6.5), 20% PEGMME500, 10% PEG20,000 , 20 mM sodium formate , 20 mM ammonium acetate, 20 mM sodium citrate tribasic dehydrate, 20 mM sodium potassium tartrate ...Details: 100 mM imidazole/MES (pH 6.5), 20% PEGMME500, 10% PEG20,000 , 20 mM sodium formate , 20 mM ammonium acetate, 20 mM sodium citrate tribasic dehydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→45.7 Å / Num. obs: 67271 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.998 / Net I/σ(I): 14.7
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 28263 / CC1/2: 0.794

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→45.7 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.838 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23148 3322 4.9 %RANDOM
Rwork0.19606 ---
obs0.1978 63910 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.028 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 4 415 5077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194772
X-RAY DIFFRACTIONr_bond_other_d0.0070.024614
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9636440
X-RAY DIFFRACTIONr_angle_other_deg1.32310640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.815568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77123.182220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41715870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1261538
X-RAY DIFFRACTIONr_chiral_restr0.1150.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215256
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021126
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8542.6072284
X-RAY DIFFRACTIONr_mcbond_other2.8532.6062283
X-RAY DIFFRACTIONr_mcangle_it3.8973.8842848
X-RAY DIFFRACTIONr_mcangle_other3.8963.8852849
X-RAY DIFFRACTIONr_scbond_it4.3293.1062488
X-RAY DIFFRACTIONr_scbond_other4.3283.1062489
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5434.4483593
X-RAY DIFFRACTIONr_long_range_B_refined8.31521.6285674
X-RAY DIFFRACTIONr_long_range_B_other8.20221.2735529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 35240 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 254 -
Rwork0.294 4688 -
obs--100 %

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