[English] 日本語
Yorodumi
- PDB-8xuw: Crystal Structure of the bromodomain of Fusarium graminearum GCN5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xuw
TitleCrystal Structure of the bromodomain of Fusarium graminearum GCN5
ComponentsHistone acetyltransferase GCN5
KeywordsTRANSCRIPTION / Bromodomain-containing protein
Function / homology
Function and homology information


negative regulation of induction of conjugation with cellular fusion / ADA complex / histone crotonyltransferase activity / SLIK (SAGA-like) complex / SAGA complex / chromosome, centromeric region / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity ...negative regulation of induction of conjugation with cellular fusion / ADA complex / histone crotonyltransferase activity / SLIK (SAGA-like) complex / SAGA complex / chromosome, centromeric region / histone H4K16 acetyltransferase activity / 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 / histone reader activity / : / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / nucleus / cytosol
Similarity search - Function
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 / Bromodomain profile. / bromo 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Histone acetyltransferase GCN5
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsLi, L. / Ran, T. / Wang, W. / Zhang, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2022YFD1700300 China
CitationJournal: To Be Published
Title: Crystal Structure of the bromodomain of Fusarium graminearum GCN5
Authors: Li, L. / Ran, T. / Wang, W. / Zhang, F.
History
DepositionJan 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone acetyltransferase GCN5


Theoretical massNumber of molelcules
Total (without water)13,9261
Polymers13,9261
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.582, 74.977, 50.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Histone acetyltransferase GCN5


Mass: 13925.575 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (fungus) / Gene: FUG_LOCUS431635, MDCFG202_LOCUS278190 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H3G405, histone acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2 M Sodium chloride,0.1 M BIS-TRIS pH5.5,25% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.58→19.91 Å / Num. obs: 17567 / % possible obs: 99.8 % / Redundancy: 12.5 % / CC1/2: 1 / Net I/σ(I): 26.9
Reflection shellResolution: 1.58→1.61 Å / Num. unique obs: 824 / CC1/2: 0.642

-
Processing

Software
NameVersionClassification
PHENIXv1.16refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→19.91 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2044 --
Rwork0.1885 --
obs-17252 99.67 %
Displacement parametersBiso mean: 26.59 Å2
Refinement stepCycle: LAST / Resolution: 1.58→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 0 162 1098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0105978
X-RAY DIFFRACTIONf_angle_d1.25251334
X-RAY DIFFRACTIONf_chiral_restr0.0731138
X-RAY DIFFRACTIONf_plane_restr0.0054176
X-RAY DIFFRACTIONf_dihedral_angle_d15.8499602

+
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