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- PDB-7vkg: Crystal structure of AF9 YEATS domain in complex with Compound 10 -

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Basic information

Entry
Database: PDB / ID: 7vkg
TitleCrystal structure of AF9 YEATS domain in complex with Compound 10
ComponentsProtein AF-9
KeywordsTRANSCRIPTION / Complex / inhibitor
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 / anterior/posterior pattern specification / hematopoietic stem cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events ...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 / anterior/posterior pattern specification / hematopoietic stem cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / lysine-acetylated histone binding / negative regulation of canonical Wnt signaling pathway / chromosome / gene expression / histone binding / molecular adaptor activity / chromatin binding / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile.
Similarity search - Domain/homology
~{N}-(4-chlorophenyl)-2-phenylmethoxy-ethanamide / Protein AF-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsLiu, Y. / Ruan, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int J Mol Sci / Year: 2022
Title: Fragment-Based Discovery of AF9 YEATS Domain Inhibitors.
Authors: Liu, Y. / Jin, R. / Lu, H. / Bian, K. / Wang, R. / Wang, L. / Gao, R. / Zhang, J. / Wu, J. / Yao, X. / Liu, X. / Liu, D. / Wang, X. / Zhang, Z. / Ruan, K.
History
DepositionSep 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein AF-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8887
Polymers16,3291
Non-polymers5596
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.381, 31.553, 59.378
Angle α, β, γ (deg.)90.000, 102.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42568
#2: Chemical ChemComp-7IV / ~{N}-(4-chlorophenyl)-2-phenylmethoxy-ethanamide


Mass: 275.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14ClNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M trimethylamine N-oxide dehydrate, 0.1 M Tris, 20% w/v PEGMME 2000, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.83→40 Å / Num. obs: 13843 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.53 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.44
Reflection shellResolution: 1.83→1.86 Å / Rmerge(I) obs: 0.652 / Num. unique obs: 13843

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Processing

Software
NameVersionClassification
REFMAC1.16refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMP

4tmp


Resolution: 1.83→40 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 603 4.69 %
Rwork0.202 --
obs0.2039 13843 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.1 Å2 / Biso mean: 26.6103 Å2 / Biso min: 13.28 Å2
Refinement stepCycle: final / Resolution: 1.83→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 36 61 1213
Biso mean--35.76 32.43 -
Num. residues----134
LS refinement shellResolution: 1.83→1.95 Å
RfactorNum. reflection% reflection
Rfree0.3591 142 -
Rwork0.294 --
obs-2567 98 %

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