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- PDB-5vnb: YEATS in complex with histone H3 -

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Basic information

Entry
Database: PDB / ID: 5vnb
TitleYEATS in complex with histone H3
Components
  • H3K23acK27ac peptide
  • YEATS domain-containing protein 4
KeywordsTRANSCRIPTION / Histone reader / YEATS domain
Function / homology
Function and homology information


modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / 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 / epigenetic regulation of gene expression ...modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / 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 / 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 / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / 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 / lysine-acetylated histone binding / 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 / structural constituent of cytoskeleton / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / mitotic cell cycle / 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) / nuclear membrane / regulation of apoptotic process / 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 / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus
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 / Histone H2A/H2B/H3 ...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
YEATS domain-containing protein 4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCho, H.J. / Cierpicki, T.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: GAS41 Recognizes Diacetylated Histone H3 through a Bivalent Binding Mode.
Authors: Cho, H.J. / Li, H. / Linhares, B.M. / Kim, E. / Ndoj, J. / Miao, H. / Grembecka, J. / Cierpicki, T.
History
DepositionApr 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / 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
Revision 1.2Oct 4, 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_2
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
K: H3K23acK27ac peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,32417
Polymers70,4095
Non-polymers91512
Water2,378132
1
A: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4893
Polymers17,3311
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8100 Å2
MethodPISA
2
B: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,99210
Polymers17,3311
Non-polymers6619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8040 Å2
MethodPISA
3
C: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4272
Polymers17,3311
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7800 Å2
MethodPISA
4
D: YEATS domain-containing protein 4
K: H3K23acK27ac peptide


Theoretical massNumber of molelcules
Total (without water)18,4162
Polymers18,4162
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-7 kcal/mol
Surface area8350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.790, 80.305, 121.663
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: 17330.924 Da / Num. of mol.: 4 / Fragment: UNP residues 1-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS4, GAS41 / Plasmid: pGST-parallel / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95619
#2: Protein/peptide H3K23acK27ac peptide


Mass: 1085.234 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Histone H3 H3K23acK27ac peptide ALY-acetylation modification on Lys residue L-peptide linking
Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.4 / Details: 1.36 M ammonium sulfate, 100 mM CHES pH 9.4

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2016
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 27276 / % possible obs: 97.5 % / Redundancy: 7 % / Net I/σ(I): 28
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1389 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VNA

5vna


Resolution: 2.4→48.67 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.422 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.254 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24771 1354 5 %RANDOM
Rwork0.18619 ---
obs0.18916 25753 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.4→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4273 0 52 132 4457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194437
X-RAY DIFFRACTIONr_bond_other_d0.0020.024156
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9566004
X-RAY DIFFRACTIONr_angle_other_deg0.9539574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0115509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83423.897213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96515738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8531519
X-RAY DIFFRACTIONr_chiral_restr0.0910.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214866
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021045
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_it4.9195.7082054
X-RAY DIFFRACTIONr_mcbond_other4.9165.7062053
X-RAY DIFFRACTIONr_mcangle_it7.3938.5262557
X-RAY DIFFRACTIONr_mcangle_other7.3928.5292558
X-RAY DIFFRACTIONr_scbond_it5.0386.0492383
X-RAY DIFFRACTIONr_scbond_other4.9056.0292364
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.398.8443421
X-RAY DIFFRACTIONr_long_range_B_refined10.52644.5324710
X-RAY DIFFRACTIONr_long_range_B_other10.53744.5244687
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 88 -
Rwork0.252 1928 -
obs--99.85 %

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