[English] 日本語
Yorodumi
- PDB-9oo9: Crystal structure of MYST acetyltransferase domain in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9oo9
TitleCrystal structure of MYST acetyltransferase domain in complex with inhibitor 6
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSFERASE/INHIBITOR / Acetyltransferase / Inhibitor / Complex / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K16 acetyltransferase activity / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / dosage compensation by inactivation of X chromosome ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K16 acetyltransferase activity / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / dosage compensation by inactivation of X chromosome / post-embryonic hemopoiesis / myeloid cell differentiation / NSL complex / negative regulation of epithelial to mesenchymal transition / negative regulation of type I interferon production / oogenesis / Formation of WDR5-containing histone-modifying complexes / NuA4 histone acetyltransferase complex / MLL1 complex / histone acetyltransferase complex / protein-lysine-acetyltransferase activity / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase / neurogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / kinetochore / regulation of autophagy / nuclear matrix / HATs acetylate histones / chromosome / 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 / zinc ion binding / nucleoplasm / 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
Chem-R7L / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHermans, S.J. / Suwandi, A. / Parker, M.W. / Baell, J.B.
Funding support Australia, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1030704 Australia
National Health and Medical Research Council (NHMRC, Australia)1080146 Australia
National Health and Medical Research Council (NHMRC, Australia)1117602 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1194263 Australia
CitationJournal: J.Med.Chem. / Year: 2026
Title: Biological Activity and Structural Biology of Current KAT6A Inhibitor Chemotypes.
Authors: Suwandi, A. / Jin, J. / Zhao, Y. / Mudududdla, R. / Gee, Y.S. / Deora, G.S. / Sun, Y. / Wei, H. / Huang, F. / He, J.S. / George, A.J. / Hermans, S.J. / Leaver, D.J. / Parker, M.W. / Baell, J.B.
History
DepositionMay 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 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)35,2209
Polymers34,4341
Non-polymers7868
Water5,008278
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)46.497, 58.035, 121.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Histone acetyltransferase KAT8 / Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / hMOF


Mass: 34433.598 Da / Num. of mol.: 1 / Mutation: A142S, L145M, T146I, K157R, S204W
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

-
Non-polymers , 5 types, 286 molecules

#2: Chemical ChemComp-R7L / 2,6-dimethoxy-N-{4-methoxy-6-[(1H-pyrazol-1-yl)methyl]-1,2-benzoxazol-3-yl}benzene-1-sulfonamide


Mass: 444.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N4O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.25 M Potassium/Sodium Tartrate, 20% PEG3350 / Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Feb 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.2→20.33 Å / Num. obs: 17192 / % possible obs: 99.36 % / Redundancy: 2 % / Biso Wilson estimate: 12.12 Å2 / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.0935 / Rpim(I) all: 0.105 / Rrim(I) all: 0.1322 / Net I/σ(I): 5.89
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2029 / Mean I/σ(I) obs: 3.09 / Num. unique obs: 1676 / CC1/2: 0.865 / CC star: 0.963 / Rpim(I) all: 0.213 / Rrim(I) all: 0.287 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20.327 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 835 4.87 %
Rwork0.1881 --
obs0.1905 17153 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→20.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 48 278 2504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082298
X-RAY DIFFRACTIONf_angle_d0.9543114
X-RAY DIFFRACTIONf_dihedral_angle_d4.3671892
X-RAY DIFFRACTIONf_chiral_restr0.058322
X-RAY DIFFRACTIONf_plane_restr0.007384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.33780.27581360.20472671X-RAY DIFFRACTION100
2.3378-2.51790.25161440.20822669X-RAY DIFFRACTION100
2.5179-2.77080.27871660.20182678X-RAY DIFFRACTION100
2.7708-3.17040.22621300.19412715X-RAY DIFFRACTION100
3.1704-3.98940.19551380.1642735X-RAY DIFFRACTION100
3.9894-20.3270.24551210.18352850X-RAY DIFFRACTION98

+
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