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- PDB-6s1r: Structure of fission yeast Mis16 bound to histone H4 -

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Basic information

Entry
Database: PDB / ID: 6s1r
TitleStructure of fission yeast Mis16 bound to histone H4
Components
  • Histone H4
  • Histone acetyltransferase type B subunit 2
KeywordsCELL CYCLE / centromere mitosis WD40 histone chaperone
Function / homology
Function and homology information


Condensation of Prophase Chromosomes / PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / : / Oxidative Stress Induced Senescence / HATs acetylate histones / CENP-A recruiting complex ...Condensation of Prophase Chromosomes / PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / : / Oxidative Stress Induced Senescence / HATs acetylate histones / CENP-A recruiting complex / SUMOylation of chromatin organization proteins / Transcriptional regulation by small RNAs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Neddylation / HDACs deacetylate histones / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape / H3-H4 histone complex chaperone activity / CENP-A containing chromatin assembly / chromosome, centromeric region / kinetochore / nucleosome assembly / nucleosome / histone binding / chromatin remodeling / protein heterodimerization activity / DNA binding / nucleus / cytoplasm
Similarity search - Function
Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold ...Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Histone acetyltransferase type B subunit 2 / Histone H4
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLefevre, S. / Korntner-Vetter, M. / Singleton, M.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome TrustFC001155 United Kingdom
Medical Research Council (United Kingdom)FC001155 United Kingdom
Cancer Research UKFC001155 United Kingdom
CitationJournal: Life Sci Alliance / Year: 2019
Title: Subunit interactions and arrangements in the fission yeast Mis16-Mis18-Mis19 complex.
Authors: Korntner-Vetter, M. / Lefevre, S. / Hu, X.W. / George, R. / Singleton, M.R.
History
DepositionJun 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase type B subunit 2
B: Histone H4


Theoretical massNumber of molelcules
Total (without water)51,8842
Polymers51,8842
Non-polymers00
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-4 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.390, 77.980, 97.510
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 Histone acetyltransferase type B subunit 2 / Kinetochore protein mis16


Mass: 48407.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: mis16, hat2, SPCC1672.10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O94244
#2: Protein/peptide Histone H4 /


Mass: 3476.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P09322
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.05 M LiSO4, 0.8 M NaH2PO4, 1.2 M K2HPO4, 0.1 M CAPS pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.8→46.22 Å / Num. obs: 39885 / % possible obs: 96.58 % / Redundancy: 2 % / Net I/σ(I): 9.36
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 3857

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S1L

6s1l


Resolution: 1.8→46.22 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.5
RfactorNum. reflection% reflection
Rfree0.2407 1921 4.82 %
Rwork0.2041 --
obs0.2059 39872 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→46.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 0 256 3480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073304
X-RAY DIFFRACTIONf_angle_d0.9094508
X-RAY DIFFRACTIONf_dihedral_angle_d3.5711963
X-RAY DIFFRACTIONf_chiral_restr0.061498
X-RAY DIFFRACTIONf_plane_restr0.005591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84510.39091220.35582584X-RAY DIFFRACTION94
1.8451-1.89490.41881180.40682505X-RAY DIFFRACTION91
1.8949-1.95070.49881030.40782132X-RAY DIFFRACTION77
1.9507-2.01370.31131510.27482719X-RAY DIFFRACTION100
2.0137-2.08560.26851450.242760X-RAY DIFFRACTION100
2.0856-2.16910.26281230.23432801X-RAY DIFFRACTION100
2.1691-2.26790.3031200.27432739X-RAY DIFFRACTION98
2.2679-2.38740.30231430.2252695X-RAY DIFFRACTION97
2.3874-2.5370.23481390.20732775X-RAY DIFFRACTION100
2.537-2.73290.25071620.19992786X-RAY DIFFRACTION100
2.7329-3.00780.24191510.19862804X-RAY DIFFRACTION100
3.0078-3.44290.21351520.17962812X-RAY DIFFRACTION100
3.4429-4.33720.20441450.16332847X-RAY DIFFRACTION99
4.3372-46.23690.19821470.16922992X-RAY DIFFRACTION100

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