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- PDB-5xtz: Crystal structure of GAS41 YEATS bound to H3K27ac peptide -

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Basic information

Entry
Database: PDB / ID: 5xtz
TitleCrystal structure of GAS41 YEATS bound to H3K27ac peptide
Components
  • THR-LYS-ALA-ALA-ARG-ALY-SER-ALA-PRO-ALA
  • YEATS domain-containing protein 4
KeywordsPROTEIN BINDING / epigenetic / histone acetylation
Function / homology
Function and homology information


modification-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication ...modification-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / : / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / structural constituent of cytoskeleton / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / mitotic cell cycle / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / regulation of apoptotic process / nuclear membrane / Estrogen-dependent gene expression / histone binding / regulation of cell cycle / cadherin binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
YEATS domain / YEATS / : / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A ...YEATS domain / 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
ACETATE ION / YEATS domain-containing protein 4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å
AuthorsLi, H.T. / Zhao, D.
Funding support China, 2items
OrganizationGrant numberCountry
Natural Science Foundation of China91519304 China
Natural Science Foundation of China81602476 China
CitationJournal: Cell Discov / Year: 2018
Title: Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity.
Authors: Hsu, C.C. / Zhao, D. / Shi, J. / Peng, D. / Guan, H. / Li, Y. / Huang, Y. / Wen, H. / Li, W. / Li, H. / Shi, X.
History
DepositionJun 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YEATS domain-containing protein 4
B: YEATS domain-containing protein 4
C: YEATS domain-containing protein 4
D: YEATS domain-containing protein 4
E: THR-LYS-ALA-ALA-ARG-ALY-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3657
Polymers76,2475
Non-polymers1182
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-16 kcal/mol
Surface area32270 Å2
2
A: YEATS domain-containing protein 4
B: YEATS domain-containing protein 4
D: YEATS domain-containing protein 4
E: THR-LYS-ALA-ALA-ARG-ALY-SER-ALA-PRO-ALA
hetero molecules

C: YEATS domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)76,3657
Polymers76,2475
Non-polymers1182
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area6810 Å2
ΔGint-26 kcal/mol
Surface area30190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.864, 80.663, 107.028
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
YEATS domain-containing protein 4 / Glioma-amplified sequence 41 / Gas41 / NuMA-binding protein 1 / NuBI1


Mass: 18800.621 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 15-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS4, GAS41 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: O95619
#2: Protein/peptide THR-LYS-ALA-ALA-ARG-ALY-SER-ALA-PRO-ALA


Mass: 1044.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate trihydrate, pH 4.6, 4.0 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 38636 / % possible obs: 99.6 % / Redundancy: 10.1 % / Net I/σ(I): 16.8
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMP

4tmp


Resolution: 2.105→49.103 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1937 5.02 %
Rwork0.1935 --
obs0.1955 38622 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.105→49.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 8 148 4862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084838
X-RAY DIFFRACTIONf_angle_d1.1096545
X-RAY DIFFRACTIONf_dihedral_angle_d12.3021804
X-RAY DIFFRACTIONf_chiral_restr0.048708
X-RAY DIFFRACTIONf_plane_restr0.006823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1046-2.15720.30541250.23172457X-RAY DIFFRACTION95
2.1572-2.21550.2581360.23512582X-RAY DIFFRACTION100
2.2155-2.28070.2851520.22712581X-RAY DIFFRACTION100
2.2807-2.35440.27041440.22622601X-RAY DIFFRACTION100
2.3544-2.43850.28121460.2292606X-RAY DIFFRACTION100
2.4385-2.53610.28711500.21742581X-RAY DIFFRACTION100
2.5361-2.65150.25931210.21172597X-RAY DIFFRACTION100
2.6515-2.79130.26511190.21482650X-RAY DIFFRACTION100
2.7913-2.96620.27071330.21682622X-RAY DIFFRACTION100
2.9662-3.19520.22971430.20022625X-RAY DIFFRACTION100
3.1952-3.51660.24491480.18642631X-RAY DIFFRACTION100
3.5166-4.02530.18351360.1792657X-RAY DIFFRACTION100
4.0253-5.07060.19041080.1482734X-RAY DIFFRACTION100
5.0706-49.11670.19391760.17572761X-RAY DIFFRACTION99

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