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- PDB-6ypc: Crystal structure of the kinetochore subunits H/I/K/T/W penta-com... -

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Basic information

Entry
Database: PDB / ID: 6ypc
TitleCrystal structure of the kinetochore subunits H/I/K/T/W penta-complex from S. cerevisiae at 2.9 angstroms
Components(Inner kinetochore subunit ...) x 5
KeywordsCELL CYCLE / kinetochore / cenp complex / centromeres / chromosome segregation
Function / homology
Function and homology information


negative regulation of kinetochore assembly / attachment of spindle microtubules to kinetochore / centromeric DNA binding / establishment of mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / DNA replication initiation / meiotic cell cycle / chromosome segregation / kinetochore / cell division ...negative regulation of kinetochore assembly / attachment of spindle microtubules to kinetochore / centromeric DNA binding / establishment of mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / DNA replication initiation / meiotic cell cycle / chromosome segregation / kinetochore / cell division / protein-containing complex binding / nucleus
Similarity search - Function
Inner kinetochore subunit CNN1 / Inner kinetochore subunit MCM22 / Inner kinetochore subunit MCM16 / Inner kinetochore subunit CTF3 / Inner kinetochore subunit WIP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBellini, D. / Zhang, Z. / Barford, D.
Funding support2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/6
Cancer Research UKC576/A14109
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Crystal structure of the Cenp-HIKHead-TW sub-module of the inner kinetochore CCAN complex.
Authors: Zhang, Z. / Bellini, D. / Barford, D.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
K: Inner kinetochore subunit MCM22
H: Inner kinetochore subunit MCM16
T: Inner kinetochore subunit CNN1
W: Inner kinetochore subunit WIP1
I: Inner kinetochore subunit CTF3


Theoretical massNumber of molelcules
Total (without water)99,1695
Polymers99,1695
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12170 Å2
ΔGint-76 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.577, 132.577, 241.676
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11K-302-

HOH

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Components

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Inner kinetochore subunit ... , 5 types, 5 molecules KHTWI

#1: Protein Inner kinetochore subunit MCM22 / CENP-K homolog / Constitutive centromere-associated network protein MCM22 / Minichromosome ...CENP-K homolog / Constitutive centromere-associated network protein MCM22 / Minichromosome maintenance protein 22


Mass: 12748.634 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: MCM22, YJR135C, J2122 / Production host: Escherichia coli (E. coli) / References: UniProt: P47167
#2: Protein/peptide Inner kinetochore subunit MCM16 / CENP-H homolog / Constitutive centromere-associated network protein MCM16 / Minichromosome ...CENP-H homolog / Constitutive centromere-associated network protein MCM16 / Minichromosome maintenance protein 16


Mass: 5153.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: MCM16, YPR046W / Production host: Escherichia coli (E. coli) / References: UniProt: Q12262
#3: Protein Inner kinetochore subunit CNN1 / CENP-T homolog / Co-purified with NNF1 protein 1 / Constitutive centromere-associated network protein CNN1


Mass: 42154.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: CNN1, YFR046C / Production host: Escherichia coli (E. coli) / References: UniProt: P43618
#4: Protein Inner kinetochore subunit WIP1 / CENP-W homolog / Constitutive centromere-associated network protein WIP1 / W-like protein 1


Mass: 10255.458 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: WIP1, YDR374W-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q2V2P8
#5: Protein Inner kinetochore subunit CTF3 / CENP-I homolog / Chromosome loss protein 3 / Chromosome transmission fidelity protein 3 / ...CENP-I homolog / Chromosome loss protein 3 / Chromosome transmission fidelity protein 3 / Constitutive centromere-associated network protein CTF3


Mass: 28856.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: CTF3, CHL3, YLR381W / Production host: Escherichia coli (E. coli) / References: UniProt: Q12748

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Non-polymers , 1 types, 7 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.22 Å3/Da / Density % sol: 70.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 M NaH2PO4 and 0.38M K2HPO4 with protein at 5.5 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9465 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9465 Å / Relative weight: 1
ReflectionResolution: 2.9→74.07 Å / Num. obs: 24344 / % possible obs: 100 % / Redundancy: 63.3 % / Biso Wilson estimate: 78.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.368 / Rpim(I) all: 0.047 / Net I/σ(I): 10
Reflection shellResolution: 2.9→3.07 Å / Num. unique obs: 3860 / CC1/2: 0.684 / Rpim(I) all: 1.826

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
PHENIX1.17.1_3660refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z08 and 3B0D

5z08

3b0d


Resolution: 2.9→68.85 Å / SU ML: 0.4099 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.3898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2829 1027 5.22 %
Rwork0.2283 18651 -
obs0.2312 19678 80.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.07 Å2
Refinement stepCycle: LAST / Resolution: 2.9→68.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4334 0 0 7 4341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00974411
X-RAY DIFFRACTIONf_angle_d1.26265975
X-RAY DIFFRACTIONf_chiral_restr0.0616712
X-RAY DIFFRACTIONf_plane_restr0.0065742
X-RAY DIFFRACTIONf_dihedral_angle_d12.6764571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.050.3617790.32481204X-RAY DIFFRACTION37.79
3.05-3.240.3396760.27951765X-RAY DIFFRACTION53.69
3.24-3.490.32211240.27682447X-RAY DIFFRACTION75.02
3.49-3.840.33531770.26343192X-RAY DIFFRACTION98.14
3.84-4.40.29132060.22173247X-RAY DIFFRACTION99.65
4.4-5.540.25311850.2073307X-RAY DIFFRACTION99.77
5.54-68.850.26141800.21153489X-RAY DIFFRACTION99.97

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