[English] 日本語
Yorodumi
- PDB-7by1: Crystal structure of GCN5 PCAF N-terminal domain -

+
Open data


ID or keywords:

Loading...

-
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


Formation of WDR5-containing histone-modifying complexes / histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / B-WICH complex positively regulates rRNA expression / : / regulation of cartilage development / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling ...Formation of WDR5-containing histone-modifying complexes / histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / B-WICH complex positively regulates rRNA expression / : / regulation of cartilage development / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / histone H4K12 acetyltransferase activity / Notch-HLH transcription pathway / histone H3K9 acetyltransferase activity / regulation of bone development / regulation of tubulin deacetylation / regulation of stem cell population maintenance / positive regulation of cardiac muscle cell differentiation / negative regulation of centriole replication / positive regulation of cell projection organization / oxoglutarate dehydrogenase complex / transcription factor TFTC complex / regulation of regulatory T cell differentiation / telencephalon development / N-acetyltransferase activity / histone H3 acetyltransferase activity / Ub-specific processing proteases / histone H3K18 acetyltransferase activity / ATAC complex / limb development / regulation of T cell activation / SAGA complex / acetyltransferase activity / midbrain development / regulation of RNA splicing / intracellular distribution of mitochondria / regulation of cell division / regulation of embryonic development / histone acetyltransferase complex / negative regulation of gluconeogenesis / long-term memory / somitogenesis / histone acetyltransferase activity / regulation of DNA repair / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of gluconeogenesis / positive regulation of cytokine production / gluconeogenesis / neural tube closure / response to nutrient levels / cellular response to nerve growth factor stimulus / regulation of protein stability / regulation of synaptic plasticity / protein modification process / histone deacetylase binding / multicellular organism growth / mitotic spindle / cellular response to tumor necrosis factor / nervous system development / heart development / fibroblast proliferation / protein phosphatase binding / DNA-binding transcription factor binding / in utero embryonic development / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / centrosome / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more