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- PDB-6s29: Structure of fission yeast Mis16-Mis19 complex -

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Basic information

Entry
Database: PDB / ID: 6s29
TitleStructure of fission yeast Mis16-Mis19 complex
Components
  • CENP-A recruiting complex protein mis19
  • Histone acetyltransferase type B subunit 2
KeywordsCELL CYCLE / centromere mitosis WD40 histone chaperone
Function / homology
Function and homology information


HATs acetylate histones / chromosome, centromeric core domain / CENP-A recruiting complex / Neddylation / HDACs deacetylate histones / H3-H4 histone complex chaperone activity / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / mitotic sister chromatid segregation ...HATs acetylate histones / chromosome, centromeric core domain / CENP-A recruiting complex / Neddylation / HDACs deacetylate histones / H3-H4 histone complex chaperone activity / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / mitotic sister chromatid segregation / chromosome, centromeric region / kinetochore / histone binding / chromatin remodeling / cell division / nucleoplasm / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats ...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 / 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
BROMIDE ION / CENP-A recruiting complex protein mis19 / Histone acetyltransferase type B subunit 2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.988 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 20, 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

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase type B subunit 2
B: CENP-A recruiting complex protein mis19
C: Histone acetyltransferase type B subunit 2
D: CENP-A recruiting complex protein mis19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,96610
Polymers111,4864
Non-polymers4796
Water13,980776
1
A: Histone acetyltransferase type B subunit 2
B: CENP-A recruiting complex protein mis19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9835
Polymers55,7432
Non-polymers2403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-9 kcal/mol
Surface area21300 Å2
MethodPISA
2
C: Histone acetyltransferase type B subunit 2
D: CENP-A recruiting complex protein mis19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9835
Polymers55,7432
Non-polymers2403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-6 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.171, 99.035, 109.880
Angle α, β, γ (deg.)90.00, 98.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone acetyltransferase type B subunit 2 / Kinetochore protein mis16


Mass: 48407.410 Da / Num. of mol.: 2
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 CENP-A recruiting complex protein mis19 / Eighteen-interacting centromere protein 1 / Kinetochore protein mis19


Mass: 7335.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mis19, eic1, kis1, SPBC27B12.02, SPBC30B4.10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O42995
#3: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 776 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.6 M NaBr, 0.1 M Tris pH 9.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.988→54.28 Å / Num. obs: 69320 / % possible obs: 89.56 % / Redundancy: 5.6 % / Net I/σ(I): 8.11
Reflection shellResolution: 1.988→2.06 Å / Num. unique obs: 3761

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S1L

6s1l


Resolution: 1.988→54.28 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.96
RfactorNum. reflection% reflection
Rfree0.2342 3556 5.14 %
Rwork0.1959 --
obs0.1979 69227 89.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.988→54.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7163 0 6 776 7945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097337
X-RAY DIFFRACTIONf_angle_d1.1069992
X-RAY DIFFRACTIONf_dihedral_angle_d7.2474383
X-RAY DIFFRACTIONf_chiral_restr0.0661108
X-RAY DIFFRACTIONf_plane_restr0.0071303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9879-2.01510.3096660.28061224X-RAY DIFFRACTION42
2.0151-2.04390.3256860.2581507X-RAY DIFFRACTION51
2.0439-2.07440.3279880.26341637X-RAY DIFFRACTION57
2.0744-2.10680.2992980.25461854X-RAY DIFFRACTION63
2.1068-2.14130.27311140.24142023X-RAY DIFFRACTION70
2.1413-2.17830.2921370.24442168X-RAY DIFFRACTION75
2.1783-2.21790.26451340.23462461X-RAY DIFFRACTION84
2.2179-2.26050.29481470.22642815X-RAY DIFFRACTION97
2.2605-2.30670.281720.22622937X-RAY DIFFRACTION100
2.3067-2.35680.27721730.23372873X-RAY DIFFRACTION100
2.3568-2.41170.27411480.22832959X-RAY DIFFRACTION100
2.4117-2.4720.29431860.22462878X-RAY DIFFRACTION100
2.472-2.53880.28111620.21732945X-RAY DIFFRACTION100
2.5388-2.61350.27541530.21592918X-RAY DIFFRACTION100
2.6135-2.69790.27741640.20272927X-RAY DIFFRACTION100
2.6979-2.79430.24571530.2052957X-RAY DIFFRACTION100
2.7943-2.90620.2381270.20762929X-RAY DIFFRACTION100
2.9062-3.03840.24821550.2092928X-RAY DIFFRACTION100
3.0384-3.19860.2321520.20252959X-RAY DIFFRACTION100
3.1986-3.3990.23951570.18922925X-RAY DIFFRACTION100
3.399-3.66140.1951670.16872932X-RAY DIFFRACTION100
3.6614-4.02970.2051550.16652970X-RAY DIFFRACTION100
4.0297-4.61250.19311500.15132944X-RAY DIFFRACTION100
4.6125-5.81030.17141660.16372976X-RAY DIFFRACTION100
5.8103-54.30370.20631460.20083025X-RAY DIFFRACTION100

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