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- PDB-5iql: Crystal structure of YEATS2 YEATS bound to H3K27cr peptide -

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Basic information

Entry
Database: PDB / ID: 5iql
TitleCrystal structure of YEATS2 YEATS bound to H3K27cr peptide
Components
  • Histone H3.1
  • YEATS domain-containing protein 2
KeywordsPROTEIN BINDING / beta sandwich
Function / homology
Function and homology information


modification-dependent protein binding / ATAC complex / regulation of tubulin deacetylation / NuA4 histone acetyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / Chromatin modifying enzymes / TBP-class protein binding / telomere organization ...modification-dependent protein binding / ATAC complex / regulation of tubulin deacetylation / NuA4 histone acetyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / Chromatin modifying enzymes / TBP-class protein binding / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / histone reader activity / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / mitotic spindle / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / regulation of cell cycle / cadherin binding / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
Three-helical bundle domain / YEATS domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A ...Three-helical bundle domain / 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
Histone H3.1 / YEATS domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLi, H. / Zhao, D. / Guan, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China91519304 China
MOST2015CB910503 China
CitationJournal: Cell Res. / Year: 2016
Title: YEATS2 is a selective histone crotonylation reader.
Authors: Zhao, D. / Guan, H. / Zhao, S. / Mi, W. / Wen, H. / Li, Y. / Zhao, Y. / Allis, C.D. / Shi, X. / Li, H.
History
DepositionMar 11, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_detector / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: YEATS domain-containing protein 2
B: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)16,6582
Polymers16,6582
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-3 kcal/mol
Surface area8810 Å2
Unit cell
Length a, b, c (Å)75.791, 75.791, 119.331
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein YEATS domain-containing protein 2


Mass: 15818.110 Da / Num. of mol.: 1 / Fragment: YEATS domain (UNP RESIDUES 201-332)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS2, KIAA1197 / Plasmid: pSUMOH10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ULM3
#2: Protein/peptide Histone H3.1


Mass: 839.960 Da / Num. of mol.: 1 / Fragment: H3 peptide (UNP RESIDUES 25-32) / Source method: obtained synthetically / Details: Kcr: lysine crotonylation / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.57 Å3/Da / Density % sol: 52.17 % / Mosaicity: 0.238 ° / Mosaicity esd: 0.005 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7 / Details: 0.1M Bis-Tris propane, 4.0 M NH4Ac, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2015 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: 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: 10507 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 40.84 Å2 / Rmerge(I) obs: 0.082 / Net I/av σ(I): 52.5 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.1412.10.7361100
2.14-2.18120.5611100
2.18-2.22120.4961100
2.22-2.2611.20.5341100
2.26-2.3110.90.575199.8
2.31-2.37120.3161100
2.37-2.4212.10.2671100
2.42-2.4912.10.241100
2.49-2.5611.20.2441100
2.56-2.65120.1661100
2.65-2.7411.80.1531100
2.74-2.8511.80.1241100
2.85-2.9811.90.0851100
2.98-3.1411.90.0721100
3.14-3.3311.30.0751100
3.33-3.5911.20.0661100
3.59-3.9510.30.0681100
3.95-4.52100.0631100
4.52-5.710.40.061100
5.7-50100.051198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMP

4tmp


Resolution: 2.1→35.221 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.77
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 1093 10.44 %Random
Rwork0.2042 ---
obs0.2094 10472 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.03 Å2 / Biso mean: 55.1106 Å2 / Biso min: 24.89 Å2
Refinement stepCycle: final / Resolution: 2.1→35.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 0 55 1210
Biso mean---48.95 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071186
X-RAY DIFFRACTIONf_angle_d0.8421603
X-RAY DIFFRACTIONf_chiral_restr0.061170
X-RAY DIFFRACTIONf_plane_restr0.006206
X-RAY DIFFRACTIONf_dihedral_angle_d13.857714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.19560.29271210.224211541275100
2.1956-2.31140.38971370.29021124126198
2.3114-2.45620.251380.216311501288100
2.4562-2.64580.27611210.237511591280100
2.6458-2.91190.30481300.24111781308100
2.9119-3.3330.24231500.219411691319100
3.333-4.19810.20871320.185311971329100
4.1981-35.22590.25461640.18011248141299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9591-0.26410.33753.12340.64423.60510.12350.3293-0.0369-0.08350.1083-0.6791-0.21711.1988-0.16230.253-0.05240.07330.617-0.05320.447221.47943.860741.5147
22.33430.44650.10782.7638-0.58783.2392-0.03020.07230.3965-0.07990.1378-0.02850.24650.0298-0.08760.29030.0293-0.05020.3098-0.03330.37979.2485-8.483139.4212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 202 through 331)A202 - 331
2X-RAY DIFFRACTION2chain 'B' and (resid 24 through 31 )B24 - 31

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