[English] 日本語
Yorodumi
- PDB-25vx: Crystal Structure of MYST histone acetyltransferase KAT6A in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 25vx
TitleCrystal Structure of MYST histone acetyltransferase KAT6A in complex with inhibitor Compound 9
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSCRIPTION / Kat6A / Inhibitor / Small molecule / Drug discovery / Acetyltransferase
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / NSL complex / histone H4K16 acetyltransferase activity / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / protein propionyltransferase activity / myeloid cell differentiation / regulation of mRNA processing ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / NSL complex / histone H4K16 acetyltransferase activity / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / protein propionyltransferase activity / myeloid cell differentiation / regulation of mRNA processing / histone H4 acetyltransferase activity / post-embryonic hemopoiesis / dosage compensation by inactivation of X chromosome / oogenesis / negative regulation of epithelial to mesenchymal transition / negative regulation of type I interferon production / Formation of WDR5-containing histone-modifying complexes / NuA4 histone acetyltransferase complex / MLL1 complex / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / protein-lysine-acetyltransferase activity / neurogenesis / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / regulation of autophagy / kinetochore / nuclear matrix / chromosome / HATs acetylate histones / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / nucleoplasm / zinc ion binding / nucleus
Similarity search - Function
: / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain ...: / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Acyl-CoA N-acyltransferase / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsNarasimhaRao, K. / Vijayshankar, N. / SumalathaRani, T. / Kalishankar, B. / Chandregowda, V. / Chandrasekar, A. / Susanta, S. / Raymond, A.N. / David, C.M.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
CitationJournal: To Be Published
Title: Crystal Structure of MYST histone acetyltransferase KAT6A in complex with Compound 9
Authors: NarasimhaRao, K. / Vijayshankar, N. / SumalathaRani, T. / Kalishankar, B. / Chandregowda, V. / Chandrasekar, A. / Susanta, S. / Raymond, A.N. / David, C.M.
History
DepositionApr 20, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone acetyltransferase KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4122
Polymers31,9461
Non-polymers4671
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.190, 57.622, 122.036
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Histone acetyltransferase KAT8 / Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / MYST-1 / Males-absent on ...Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / MYST-1 / Males-absent on the first protein homolog / hMOF / Protein acetyltransferase KAT8 / Protein propionyltransferase KAT8


Mass: 31945.830 Da / Num. of mol.: 1 / Mutation: Y579H,A645S,L648M,T649I,K660R,I702N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT8, MOF, MYST1, PP7073 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H7Z6, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-A1MGC / 2,6-dimethoxy-~{N}-(5-phenyl-3,4-dihydro-2~{H}-pyrano[2,3-e][1,2]benzoxazol-9-yl)benzenesulfonamide


Mass: 466.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22N2O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sod. Malonate, pH 6.0, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→61.19 Å / Num. obs: 15264 / % possible obs: 99.5 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.6
Reflection shellResolution: 2.29→2.37 Å / Rmerge(I) obs: 0.305 / Num. unique obs: 1397 / CC1/2: 0.983

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
CrystalCleardata reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→61.02 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.896 / SU B: 7.256 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26583 776 5.1 %RANDOM
Rwork0.1992 ---
obs0.2026 14439 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.527 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0 Å2
2--0.24 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.29→61.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 45 87 2315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192368
X-RAY DIFFRACTIONr_bond_other_d0.0050.0222
X-RAY DIFFRACTIONr_angle_refined_deg1.9941.9823213
X-RAY DIFFRACTIONr_angle_other_deg1.922347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.015273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85223.981103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44915409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.854158
X-RAY DIFFRACTIONr_chiral_restr0.1350.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211784
X-RAY DIFFRACTIONr_gen_planes_other0.0080.0211
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_it3.173.1521095
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.0154.7041367
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2743.5411273
X-RAY DIFFRACTIONr_scbond_other3.6613.14738
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9844.72855
X-RAY DIFFRACTIONr_long_range_B_refined12.36943.9163768
X-RAY DIFFRACTIONr_long_range_B_other9.75733.55399
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 54 -
Rwork0.245 968 -
obs--93.59 %

+
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