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- PDB-6qld: Structure of inner kinetochore CCAN-Cenp-A complex -

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Entry
Database: PDB / ID: 6qld
TitleStructure of inner kinetochore CCAN-Cenp-A complex
Components
  • (DNA (125-MER)) x 2
  • (Histone H2A.1) x 2
  • (Histone H3-like centromeric protein ...) x 2
  • (Inner kinetochore subunit ...) x 12
  • Histone H2B.1
  • Histone H2B.2
  • Histone H4
KeywordsDNA BINDING PROTEIN / inner kinetochore / DNA / nucleosome
Function / homology
Function and homology information


HATs acetylate histones / Estrogen-dependent gene expression / SUMOylation of chromatin organization proteins / RMTs methylate histone arginines / HDMs demethylate histones / Oxidative Stress Induced Senescence / Condensation of Prophase Chromosomes / protein localization to CENP-A containing chromatin / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / Mis6-Sim4 complex ...HATs acetylate histones / Estrogen-dependent gene expression / SUMOylation of chromatin organization proteins / RMTs methylate histone arginines / HDMs demethylate histones / Oxidative Stress Induced Senescence / Condensation of Prophase Chromosomes / protein localization to CENP-A containing chromatin / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / Mis6-Sim4 complex / COMA complex / 2-micrometer circle DNA / establishment of meiotic sister chromatid cohesion / maintenance of meiotic sister chromatid cohesion / 2-micrometer plasmid partitioning / centromere complex assembly / meiotic sister chromatid segregation / CENP-A containing nucleosome / transfer RNA gene-mediated silencing / attachment of spindle microtubules to kinetochore involved in homologous chromosome segregation / attachment of spindle microtubules to kinetochore / sexual sporulation resulting in formation of a cellular spore / ascospore formation / centromeric DNA binding / establishment of mitotic sister chromatid cohesion / attachment of mitotic spindle microtubules to kinetochore / histone H3-K79 methylation / condensed nuclear chromosome outer kinetochore / protein localization to chromosome, centromeric region / kinetochore assembly / chromatin assembly or disassembly / replication fork protection complex / condensed nuclear chromosome kinetochore / spindle pole body / postreplication repair / protein localization to kinetochore / condensed nuclear chromosome, centromeric region / DNA replication initiation / rRNA transcription / condensed chromosome kinetochore / mitotic spindle assembly checkpoint / mitotic sister chromatid segregation / nuclear nucleosome / nucleosomal DNA binding / mitotic spindle organization / kinetochore / chromosome segregation / meiotic cell cycle / nucleosome assembly / nucleosome / chromatin organization / sequence-specific DNA binding / protein-containing complex binding / cell division / nuclear chromatin / DNA repair / structural molecule activity / protein heterodimerization activity / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Histone H2A, C-terminal domain / Histone H2B / Histone H2A/H2B/H3 / Histone H2A signature. / C-terminus of histone H2A / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Histone H2A / Histone H4 / Histone H3/CENP-A / Centromere protein Chl4/mis15/CENP-N ...Histone H2A, C-terminal domain / Histone H2B / Histone H2A/H2B/H3 / Histone H2A signature. / C-terminus of histone H2A / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Histone H2A / Histone H4 / Histone H3/CENP-A / Centromere protein Chl4/mis15/CENP-N / CENP-T/Histone H4, histone fold / Core histone H2A/H2B/H3/H4 / Centromere kinetochore component CENP-T histone fold / Kinetochore protein CHL4 like / Cnl2/NKP2 family protein / Histone H2A conserved site / Histone H4 signature. / Histone H2B signature. / Mif2/CENP-C like / Mif2/cnp3, N-terminal / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C cupin domain / Histone H4, conserved site / Histone-fold / Kinetochore subunit Nkp2/Cnl2 / Centromere protein O / Histone H3 signature 2. / RmlC-like jelly roll fold / Cenp-O kinetochore centromere component
Inner kinetochore subunit NKP1 / Inner kinetochore subunit MCM16 / Inner kinetochore subunit MCM21 / Inner kinetochore subunit NKP2 / Inner kinetochore subunit CTF19 / Inner kinetochore subunit OKP1 / Inner kinetochore subunit MCM22 / Inner kinetochore subunit AME1 / Inner kinetochore subunit CHL4 / Inner kinetochore subunit IML3 ...Inner kinetochore subunit NKP1 / Inner kinetochore subunit MCM16 / Inner kinetochore subunit MCM21 / Inner kinetochore subunit NKP2 / Inner kinetochore subunit CTF19 / Inner kinetochore subunit OKP1 / Inner kinetochore subunit MCM22 / Inner kinetochore subunit AME1 / Inner kinetochore subunit CHL4 / Inner kinetochore subunit IML3 / Histone H3-like centromeric protein CSE4 / Inner kinetochore subunit MIF2 / Histone H2A.1 / Histone H4 / Histone H2B.2 / Histone H2B.1 / Inner kinetochore subunit CTF3
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.15 Å
AuthorsYan, K. / Yang, J. / Zhang, Z. / McLaughlin, S.H. / Chang, L. / Fasci, D. / Heck, A.J.R. / Barford, D.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
European CommissionINFRAIA project Epic-XS (Project 823839)
CitationJournal: Nature / Year: 2019
Title: Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome.
Authors: Kaige Yan / Jing Yang / Ziguo Zhang / Stephen H McLaughlin / Leifu Chang / Domenico Fasci / Ann E Ehrenhofer-Murray / Albert J R Heck / David Barford /
Abstract: In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized ...In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized Cenp-A nucleosomes, function to connect centromeric chromatin to microtubules of the mitotic spindle. Whereas the centromeres of vertebrate chromosomes comprise millions of DNA base pairs and attach to multiple microtubules, the simple point centromeres of budding yeast are connected to individual microtubules. All 16 budding yeast chromosomes assemble complete kinetochores using a single Cenp-A nucleosome (Cenp-A), each of which is perfectly centred on its cognate centromere. The inner and outer kinetochore modules are responsible for interacting with centromeric chromatin and microtubules, respectively. Here we describe the cryo-electron microscopy structure of the Saccharomyces cerevisiae inner kinetochore module, the constitutive centromere associated network (CCAN) complex, assembled onto a Cenp-A nucleosome (CCAN-Cenp-A). The structure explains the interdependency of the constituent subcomplexes of CCAN and shows how the Y-shaped opening of CCAN accommodates Cenp-A to enable specific CCAN subunits to contact the nucleosomal DNA and histone subunits. Interactions with the unwrapped DNA duplex at the two termini of Cenp-A are mediated predominantly by a DNA-binding groove in the Cenp-L-Cenp-N subcomplex. Disruption of these interactions impairs assembly of CCAN onto Cenp-A. Our data indicate a mechanism of Cenp-A nucleosome recognition by CCAN and how CCAN acts as a platform for assembly of the outer kinetochore to link centromeres to the mitotic spindle for chromosome segregation.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release

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Assembly

Deposited unit
C: Inner kinetochore subunit MIF2
G: DNA (125-MER)
H: Inner kinetochore subunit MCM16
I: Inner kinetochore subunit CTF3
J: DNA (125-MER)
K: Inner kinetochore subunit MCM22
L: Inner kinetochore subunit IML3
N: Inner kinetochore subunit CHL4
O: Inner kinetochore subunit MCM21
P: Inner kinetochore subunit CTF19
Q: Inner kinetochore subunit OKP1
U: Inner kinetochore subunit AME1
Y: Inner kinetochore subunit NKP1
Z: Inner kinetochore subunit NKP2
a: Histone H3-like centromeric protein CSE4
b: Histone H4
d: Histone H2B.2
e: Histone H3-like centromeric protein CSE4
f: Histone H4
g: Histone H2A.1
h: Histone H2B.1
i: Histone H2A.1


Theoretical massNumber of molelcules
Total (without water)471,67022
Polymers471,67022
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area109030 Å2
ΔGint-787 kcal/mol
Surface area183540 Å2
MethodPISA

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Components

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Inner kinetochore subunit ... , 12 types, 12 molecules CHIKLNOPQUYZ

#1: Protein/peptide Inner kinetochore subunit MIF2 / CENP-C homolog / Constitutive centromere-associated network protein MIF2 / Mitotic fidelity of chromosome transmission protein 2


Mass: 2754.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MIF2, YKL089W / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35201
#3: Protein/peptide Inner kinetochore subunit MCM16 / CENP-H homolog / Constitutive centromere-associated network protein MCM16 / Minichromosome maintenance protein 16


Mass: 15815.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MCM16, YPR046W / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12262
#4: Protein/peptide Inner kinetochore subunit CTF3 / CENP-I homolog / Chromosome loss protein 3 / Chromosome transmission fidelity protein 3 / Constitutive centromere-associated network protein CTF3


Mass: 47222.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CTF3, CHL3, YLR381W / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12748
#6: Protein/peptide Inner kinetochore subunit MCM22 / CENP-K homolog / Constitutive centromere-associated network protein MCM22 / Minichromosome maintenance protein 22


Mass: 14082.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MCM22, YJR135C, J2122 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P47167
#7: Protein/peptide Inner kinetochore subunit IML3 / CENP-L homolog / Constitutive centromere-associated network protein IML3 / Increased minichromosome loss protein 3 / Minichromosome maintenance protein 19


Mass: 27644.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: IML3, MCM19, YBR107C, YBR0836 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38265
#8: Protein/peptide Inner kinetochore subunit CHL4 / CENP-N homolog / Chromosome loss protein 4 / Chromosome transmission fidelity protein 17 / Constitutive centromere-associated network protein CHL4 / Minichromosome maintenance protein 17


Mass: 51642.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CHL4, CTF17, MCM17, YDR254W, YD9320A.04 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38907
#9: Protein/peptide Inner kinetochore subunit MCM21 / CENP-O homolog / Chromosome transmission fidelity protein 5 / Constitutive centromere-associated network protein MCM21 / Minichromosome maintenance protein 21


Mass: 24746.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MCM21, CTF5, YDR318W / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q06675
#10: Protein/peptide Inner kinetochore subunit CTF19 / CENP-P homolog / Chromosome transmission fidelity protein 19 / Constitutive centromere-associated network protein CTF19 / Minichromosome maintenance protein 18


Mass: 31659.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CTF19, MCM18, YPL018W, LPB13W / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q02732
#11: Protein/peptide Inner kinetochore subunit OKP1 / CENP-Q homolog / Constitutive centromere-associated network protein OKP1 / Outer kinetochore protein 1


Mass: 27358.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: OKP1, YGR179C / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53298
#12: Protein/peptide Inner kinetochore subunit AME1 / Associated with microtubules and essential protein 1 / CENP-U homolog / Constitutive centromere-associated network protein AME1


Mass: 22157.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: AME1, ARP100, YBR211C, YBR1458 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38313
#13: Protein/peptide Inner kinetochore subunit NKP1 / Constitutive centromere-associated network protein NKP1 / Non-essential kinetochore protein 1


Mass: 26875.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NKP1, YDR383C / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12493
#14: Protein/peptide Inner kinetochore subunit NKP2 / Constitutive centromere-associated network protein NKP2 / Non-essential kinetochore protein 2


Mass: 17631.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NKP2, YLR315W / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q06162

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DNA chain , 2 types, 2 molecules GJ

#2: DNA chain DNA (125-MER)


Mass: 38030.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#5: DNA chain DNA (125-MER)


Mass: 38510.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Histone H3-like centromeric protein ... , 2 types, 2 molecules ae

#15: Protein/peptide Histone H3-like centromeric protein CSE4 / CENP-A homolog / Chromosome segregation protein 4


Mass: 10535.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CSE4, CSL2, YKL049C, YKL262 / Production host: Escherichia coli (E. coli) / References: UniProt: P36012
#18: Protein/peptide Histone H3-like centromeric protein CSE4 / CENP-A homolog / Chromosome segregation protein 4


Mass: 13715.144 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CSE4, CSL2, YKL049C, YKL262 / Production host: Escherichia coli (E. coli) / References: UniProt: P36012

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Protein/peptide , 5 types, 6 molecules bfdghi

#16: Protein/peptide Histone H4 /


Mass: 8897.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli (E. coli) / References: UniProt: P02309
#17: Protein/peptide Histone H2B.2


Mass: 10342.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HTB2, H2B2, YBL002W, YBL0104 / Production host: Escherichia coli (E. coli) / References: UniProt: P02294
#19: Protein/peptide Histone H2A.1


Mass: 11546.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HTA1, H2A1, SPT11, YDR225W, YD9934.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P04911
#20: Protein/peptide Histone H2B.1 / Suppressor of Ty protein 12


Mass: 10413.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C / Production host: Escherichia coli (E. coli) / References: UniProt: P02293
#21: Protein/peptide Histone H2A.1


Mass: 11190.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HTA1, H2A1, SPT11, YDR225W, YD9934.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P04911

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component

Type: COMPLEX

IDNameEntity IDParent-IDSource
1Inner kinetochore CCAN complex assembled onto a centromeric nucleosome1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 170MULTIPLE SOURCES
2kinetochore1, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 141RECOMBINANT
3DNA2, 51RECOMBINANT
4HistonesHistone15, 16, 17, 18, 19, 20, 211RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Saccharomyces cerevisiae (strain ATCC 204508 / S288c) cerevisiae (yeast)559292
33Escherichia coli (E. coli)562
44Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Trichoplusia ni (cabbage looper)7111
33Escherichia coli (E. coli)562
44Escherichia coli (E. coli)562
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 32 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145783 / Symmetry type: POINT
RefinementHighest resolution: 4.15 Å / Stereochemistry target values: CDL v1.2
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.00429358
f_angle_d0.761340836
f_chiral_restr0.04564882
f_plane_restr0.00564276
f_dihedral_angle_d14.845116896

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