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- PDB-9arr: Crystal structure of AF9 YEATS domain in complex with dicrotonyla... -

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Basic information

Entry
Database: PDB / ID: 9arr
TitleCrystal structure of AF9 YEATS domain in complex with dicrotonylated at K1007 and K1014 MOZ
Components
  • Histone acetyltransferase KAT6A
  • Protein AF-9
KeywordsTRANSCRIPTION / AF9 / MOZ / YEATS / crotonylation / Chromatin
Function / homology
Function and homology information


modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / histone H3 acetyltransferase activity / myeloid cell differentiation / anterior/posterior pattern specification / MOZ/MORF histone acetyltransferase complex / regulation of developmental process ...modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / histone H3 acetyltransferase activity / myeloid cell differentiation / anterior/posterior pattern specification / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / protein acetylation / histone acetyltransferase activity / acetyltransferase activity / hematopoietic stem cell differentiation / chromosome organization / 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 / RNA Polymerase II Transcription Elongation / histone acetyltransferase / Formation of RNA Pol II elongation complex / Regulation of TP53 Activity through Acetylation / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / regulation of signal transduction by p53 class mediator / : / transcription coregulator activity / negative regulation of canonical Wnt signaling pathway / PML body / cellular senescence / nucleosome / nucleosome assembly / HATs acetylate histones / chromosome / gene expression / DNA-binding transcription factor binding / molecular adaptor activity / histone binding / transcription coactivator activity / nuclear speck / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / : / YEATS superfamily / YEATS family ...: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / : / YEATS superfamily / YEATS family / YEATS domain profile. / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / NITRATE ION / DI(HYDROXYETHYL)ETHER / Protein AF-9 / Histone acetyltransferase KAT6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSelvam, K. / Kutateladze, T.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL151334 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: A multivalent engagement of ENL with MOZ.
Authors: Becht, D.C. / Selvam, K. / Lachance, C. / Cote, V. / Li, K. / Nguyen, M.C. / Pareek, A. / Shi, X. / Wen, H. / Blanco, M.A. / Cote, J. / Kutateladze, T.G.
History
DepositionFeb 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 30, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein AF-9
B: Protein AF-9
C: Histone acetyltransferase KAT6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,10314
Polymers34,3673
Non-polymers73611
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-24 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.364, 49.021, 78.133
Angle α, β, γ (deg.)90.00, 113.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein Protein AF-9 / ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated ...ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated to chromosome 3 protein / YEATS domain-containing protein 3


Mass: 16328.885 Da / Num. of mol.: 2 / Fragment: YEATS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Production host: Escherichia coli (E. coli) / References: UniProt: P42568
#2: Protein/peptide Histone acetyltransferase KAT6A / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 3 / MYST-3 / Monocytic leukemia zinc finger protein / Runt- ...MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 3 / MYST-3 / Monocytic leukemia zinc finger protein / Runt-related transcription factor-binding protein 2 / Zinc finger protein 220


Mass: 1709.146 Da / Num. of mol.: 1 / Fragment: residues 1005-1017 (Uniprot numbering) / Source method: obtained synthetically
Details: residues K1007 and K1014 crotonylated (Uniprot numbering)
Source: (synth.) Homo sapiens (human) / References: UniProt: Q92794, histone acetyltransferase

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Non-polymers , 5 types, 138 molecules

#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.66 Å3/Da / Density % sol: 66.39 %
Crystal growTemperature: 291 K / Method: microbatch / Details: 0.2 M Lithium nitrate pH 7.1, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0722 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.1→45.97 Å / Num. obs: 27648 / % possible obs: 94.2 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.034 / Rrim(I) all: 0.066 / Χ2: 0.51 / Net I/σ(I): 8.7
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 99.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.632 / Num. measured all: 7865 / Num. unique obs: 2370 / CC1/2: 0.867 / Rpim(I) all: 0.407 / Rrim(I) all: 0.754 / Χ2: 0.47 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.758 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24748 1318 4.9 %RANDOM
Rwork0.20307 ---
obs0.20529 25539 91.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.129 Å2
Baniso -1Baniso -2Baniso -3
1--3.71 Å2-0 Å2-0.37 Å2
2--5.99 Å2-0 Å2
3----1.42 Å2
Refinement stepCycle: 1 / Resolution: 2.1→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 49 127 2598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122534
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162415
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.6823400
X-RAY DIFFRACTIONr_angle_other_deg0.6261.5935583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5165286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.645527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8410436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022894
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02598
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_it5.3184.5451153
X-RAY DIFFRACTIONr_mcbond_other5.284.5461153
X-RAY DIFFRACTIONr_mcangle_it7.0938.1221436
X-RAY DIFFRACTIONr_mcangle_other7.0928.1251437
X-RAY DIFFRACTIONr_scbond_it7.0855.3171381
X-RAY DIFFRACTIONr_scbond_other7.0825.3181382
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.1659.3141965
X-RAY DIFFRACTIONr_long_range_B_refined12.87948.792686
X-RAY DIFFRACTIONr_long_range_B_other12.89948.372676
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 109 -
Rwork0.329 2026 -
obs--99.49 %

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