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- PDB-7r5s: Structure of the human CCAN bound to alpha satellite DNA -

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Entry
Database: PDB / ID: 7r5s
TitleStructure of the human CCAN bound to alpha satellite DNA
Components
  • (Centromere protein ...) x 15
  • (DNA (66-MER)) x 2
KeywordsCELL CYCLE / Chromosome / kinetochore / cell division / centromere
Function / homology
Function and homology information


FANCM-MHF complex / Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / : / kinetochore organization / Fanconi anaemia nuclear complex / metaphase chromosome alignment / kinetochore binding / CENP-A containing chromatin assembly / sex differentiation ...FANCM-MHF complex / Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / : / kinetochore organization / Fanconi anaemia nuclear complex / metaphase chromosome alignment / kinetochore binding / CENP-A containing chromatin assembly / sex differentiation / resolution of meiotic recombination intermediates / chordate embryonic development / negative regulation of epithelial cell apoptotic process / kinetochore assembly / inner kinetochore / replication fork processing / mitotic sister chromatid segregation / chromosome, centromeric region / chromosome organization / interstrand cross-link repair / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / NRIF signals cell death from the nucleus / Resolution of Sister Chromatid Cohesion / positive regulation of protein ubiquitination / positive regulation of epithelial cell proliferation / mitotic spindle organization / chromosome segregation / Fanconi Anemia Pathway / RHO GTPases Activate Formins / PKR-mediated signaling / kinetochore / centriolar satellite / nuclear matrix / Separation of Sister Chromatids / mitotic cell cycle / actin cytoskeleton / chromosome / cell adhesion / nuclear body / protein heterodimerization activity / cell division / DNA repair / apoptotic process / DNA damage response / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / signal transduction / DNA binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Centromere protein W / : / CENP-W protein / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Centromere subunit L / Centromere protein L / Centromere protein R / Centromere protein Q ...Centromere protein W / : / CENP-W protein / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Centromere subunit L / Centromere protein L / Centromere protein R / Centromere protein Q / Centromere protein P / Kinetochore component, CENP-R / CENP-Q, a CENPA-CAD centromere complex subunit / CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P / Centromere protein H, C-terminal / Centromere protein Cenp-M / Centromere protein Cenp-K / Centromere protein H / Centromere protein H (CENP-H) / Centromere protein M (CENP-M) / Centromere-associated protein K / Centromere protein I / Mis6 / Centromere protein U / CENP-A nucleosome associated complex (NAC) subunit / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / Centromere protein O / : / Cenp-O kinetochore centromere component / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like / Histone, subunit A / Histone, subunit A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Centromere protein X / Centromere protein R / Centromere protein W / Centromere protein P / Centromere protein U / Centromere protein Q / Centromere protein L ...: / DNA / DNA (> 10) / Centromere protein X / Centromere protein R / Centromere protein W / Centromere protein P / Centromere protein U / Centromere protein Q / Centromere protein L / Centromere protein S / Centromere protein I / Centromere protein T / Centromere protein N / Centromere protein K / Centromere protein O / Centromere protein H / Centromere protein M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsYatskevich, S. / Muir, K.W. / Bellini, D. / Zhang, Z. / Yang, J. / Tischer, T. / Predin, M. / Dendooven, T. / McLaughlin, S.H. / Barford, D.
Funding support United Kingdom, Germany, 3items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
Boehringer Ingelheim Fonds (BIF) Germany
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Science / Year: 2022
Title: Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome.
Authors: Stanislau Yatskevich / Kyle W Muir / Dom Bellini / Ziguo Zhang / Jing Yang / Thomas Tischer / Masa Predin / Tom Dendooven / Stephen H McLaughlin / David Barford /
Abstract: Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron ...Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron microscopy structures of the human inner kinetochore constitutive centromere associated network (CCAN) complex bound to CENP-A reconstituted onto α-satellite DNA. CCAN forms edge-on contacts with CENP-A, and a linker DNA segment of the α-satellite repeat emerges from the fully wrapped end of the nucleosome to thread through the central CENP-LN channel that tightly grips the DNA. The CENP-TWSX histone-fold module further augments DNA binding and partially wraps the linker DNA in a manner reminiscent of canonical nucleosomes. Our study suggests that the topological entrapment of the linker DNA by CCAN provides a robust mechanism by which kinetochores withstand both pushing and pulling forces exerted by the mitotic spindle.
History
DepositionFeb 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: 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 1.2Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Centromere protein H
I: Centromere protein I
J: DNA (66-MER)
K: Centromere protein K
L: Centromere protein L
M: Centromere protein M
N: Centromere protein N
O: Centromere protein O
P: Centromere protein P
Q: Centromere protein Q
U: Centromere protein U
R: Centromere protein R
T: Centromere protein T
W: Centromere protein W
S: Centromere protein S
X: Centromere protein X
i: DNA (66-MER)


Theoretical massNumber of molelcules
Total (without water)539,11317
Polymers539,11317
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Centromere protein ... , 15 types, 15 molecules HIKLMNOPQURTWSX

#1: Protein Centromere protein H / CENP-H / Interphase centromere complex protein 35


Mass: 28520.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPH, ICEN35 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H3R5
#2: Protein Centromere protein I / CENP-I / FSH primary response protein 1 / Follicle-stimulating hormone primary response protein / ...CENP-I / FSH primary response protein 1 / Follicle-stimulating hormone primary response protein / Interphase centromere complex protein 19 / Leucine-rich primary response protein 1


Mass: 86820.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPI, FSHPRH1, ICEN19, LRPR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92674
#4: Protein Centromere protein K / CENP-K / Interphase centromere complex protein 37 / Protein AF-5alpha / p33


Mass: 31696.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPK, ICEN37, FKSG14 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BS16
#5: Protein Centromere protein L / CENP-L / Interphase centromere complex protein 33


Mass: 39039.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPL, C1orf155, ICEN33 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N0S6
#6: Protein Centromere protein M / CENP-M / Interphase centromere complex protein 39 / Proliferation-associated nuclear element protein 1


Mass: 19761.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPM, C22orf18, ICEN39, PANE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NSP4
#7: Protein Centromere protein N / CENP-N / Interphase centromere complex protein 32


Mass: 39609.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPN, C16orf60, ICEN32, BM-309 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96H22
#8: Protein Centromere protein O / CENP-O / Interphase centromere complex protein 36


Mass: 33830.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPO, ICEN36, MCM21R / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BU64
#9: Protein Centromere protein P / CENP-P


Mass: 33210.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6IPU0
#10: Protein Centromere protein Q / CENP-Q


Mass: 30648.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPQ, C6orf139 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7L2Z9
#11: Protein Centromere protein U / CENP-U / Centromere protein of 50 kDa / CENP-50 / Interphase centromere complex protein 24 / KSHV ...CENP-U / Centromere protein of 50 kDa / CENP-50 / Interphase centromere complex protein 24 / KSHV latent nuclear antigen-interacting protein 1 / MLF1-interacting protein / Polo-box-interacting protein 1


Mass: 47609.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPU, ICEN24, KLIP1, MLF1IP, PBIP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q71F23
#12: Protein Centromere protein R / CENP-R / Beta-3-endonexin / Integrin beta-3-binding protein / Nuclear receptor-interacting factor 3


Mass: 20228.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3BP, CENPR, NRIF3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13352
#13: Protein Centromere protein T / CENP-T / Interphase centromere complex protein 22


Mass: 60502.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPT, C16orf56, ICEN22 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96BT3
#14: Protein Centromere protein W / CENP-W / Cancer-up-regulated gene 2 protein


Mass: 10087.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPW, C6orf173, CUG2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5EE01
#15: Protein Centromere protein S / CENP-S / Apoptosis-inducing TAF9-like domain-containing protein 1 / FANCM-associated histone fold ...CENP-S / Apoptosis-inducing TAF9-like domain-containing protein 1 / FANCM-associated histone fold protein 1 / FANCM-interacting histone fold protein 1 / Fanconi anemia-associated polypeptide of 16 kDa


Mass: 15917.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPS, APITD1, FAAP16, MHF1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N2Z9
#16: Protein Centromere protein X / CENP-X / FANCM-associated histone fold protein 2 / FANCM-interacting histone fold protein 2 / ...CENP-X / FANCM-associated histone fold protein 2 / FANCM-interacting histone fold protein 2 / Fanconi anemia-associated polypeptide of 10 kDa / Retinoic acid-inducible gene D9 protein homolog / Stimulated by retinoic acid gene 13 protein homolog


Mass: 8972.415 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPX, FAAP10, MHF2, STRA13 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8MT69

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DNA chain , 2 types, 2 molecules Ji

#3: DNA chain DNA (66-MER)


Mass: 16459.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 36349
#17: DNA chain DNA (66-MER)


Mass: 16197.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 36349

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Non-polymers , 1 types, 1 molecules

#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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

ComponentName: Human CCAN complex with bound alpha-satellite DNA / Type: COMPLEX / Entity ID: #1-#16 / Source: MULTIPLE SOURCES
Buffer solutionpH: 7.8
SpecimenEmbedding 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 FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123677 / Symmetry type: POINT

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