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- PDB-6mim: Crystal structure of AF9 YEATS domain Y78W mutant in complex with... -

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Basic information

Entry
Database: PDB / ID: 6mim
TitleCrystal structure of AF9 YEATS domain Y78W mutant in complex with histone H3K9cr
Components
  • Histone H3K9cr
  • Protein AF-9
KeywordsTRANSCRIPTION / Epigenetic / Histone reader
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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / RNA Polymerase II Transcription Elongation ...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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / transcription elongation factor complex / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / negative regulation of canonical Wnt signaling pathway / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromosome / gene expression / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / molecular adaptor activity / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
YEATS domain / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...YEATS domain / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein AF-9 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.525 Å
AuthorsVann, K.R. / Klein, B.J. / Kutateladze, T.G.
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights into the pi-pi-pi stacking mechanism and DNA-binding activity of the YEATS domain.
Authors: Klein, B.J. / Vann, K.R. / Andrews, F.H. / Wang, W.W. / Zhang, J. / Zhang, Y. / Beloglazkina, A.A. / Mi, W. / Li, Y. / Li, H. / Shi, X. / Kutateladze, A.G. / Strahl, B.D. / Liu, W.R. / Kutateladze, T.G.
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein AF-9
C: Protein AF-9
B: Histone H3K9cr
D: Histone H3K9cr


Theoretical massNumber of molelcules
Total (without water)35,3914
Polymers35,3914
Non-polymers00
Water2,468137
1
A: Protein AF-9
B: Histone H3K9cr


Theoretical massNumber of molelcules
Total (without water)17,6952
Polymers17,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein AF-9
D: Histone H3K9cr


Theoretical massNumber of molelcules
Total (without water)17,6952
Polymers17,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.159, 59.697, 155.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 16634.195 Da / Num. of mol.: 2 / Fragment: YEATS domain residues 1-138 / Mutation: Y78W
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 H3K9cr


Mass: 1061.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 6.0, 20%(w/v) PEG 6000, and 10 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. obs: 13056 / % possible obs: 94.3 % / Redundancy: 10.8 % / Rsym value: 0.099 / Net I/σ(I): 33.5
Reflection shellResolution: 2.53→2.62 Å / Rsym value: 0.415

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMP

4tmp


Resolution: 2.525→47.338 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.53
RfactorNum. reflection% reflection
Rfree0.2637 1273 9.95 %
Rwork0.2029 --
obs0.209 12794 92.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.525→47.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 0 137 2539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122483
X-RAY DIFFRACTIONf_angle_d1.3533347
X-RAY DIFFRACTIONf_dihedral_angle_d26.898952
X-RAY DIFFRACTIONf_chiral_restr0.07341
X-RAY DIFFRACTIONf_plane_restr0.009438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5251-2.62620.3851930.2813826X-RAY DIFFRACTION62
2.6262-2.74580.35791190.30191092X-RAY DIFFRACTION81
2.7458-2.89050.3111320.26491243X-RAY DIFFRACTION92
2.8905-3.07160.32361510.25581346X-RAY DIFFRACTION98
3.0716-3.30870.3031530.23391366X-RAY DIFFRACTION100
3.3087-3.64150.28021500.19971369X-RAY DIFFRACTION100
3.6415-4.16820.25621550.1821379X-RAY DIFFRACTION100
4.1682-5.25040.19621560.14971410X-RAY DIFFRACTION100
5.2504-47.34630.23951640.19751490X-RAY DIFFRACTION100

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