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- PDB-7ywx: Structure of the human CCAN CENP-A alpha-satellite complex -

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Database: PDB / ID: 7ywx
TitleStructure of the human CCAN CENP-A alpha-satellite complex
Components
  • (Centromere protein ...) x 16
  • (DNA (171-MER)) x 2
  • Histone H2A type 1-C
  • Histone H2B type 1-C/E/F/G/I
  • Histone H3-like centromeric protein A
  • Histone H4
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 / centromere complex assembly / kinetochore organization / Fanconi anaemia nuclear complex / spindle attachment to meiosis I kinetochore / metaphase chromosome alignment / kinetochore binding / centromeric DNA binding ...FANCM-MHF complex / Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / centromere complex assembly / kinetochore organization / Fanconi anaemia nuclear complex / spindle attachment to meiosis I kinetochore / metaphase chromosome alignment / kinetochore binding / centromeric DNA binding / CENP-A containing chromatin assembly / sex differentiation / resolution of meiotic recombination intermediates / chordate embryonic development / protein localization to chromosome, centromeric region / negative regulation of epithelial cell apoptotic process / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / inner kinetochore / condensed chromosome, centromeric region / replication fork processing / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / mitotic cytokinesis / chromosome, centromeric region / centriolar satellite / Replacement of protamines by nucleosomes in the male pronucleus / chromosome organization / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / arachidonate metabolic process / lipid oxidation / interstrand cross-link repair / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Mitotic Prometaphase / positive regulation of epithelial cell proliferation / EML4 and NUDC in mitotic spindle formation / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / Resolution of Sister Chromatid Cohesion / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / NRIF signals cell death from the nucleus / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / mitotic spindle organization / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / positive regulation of protein ubiquitination / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / chromosome segregation / RNA Polymerase I Promoter Escape / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / Fanconi Anemia Pathway / Transcriptional regulation of granulopoiesis / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / PKR-mediated signaling / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / kinetochore / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / structural constituent of chromatin / Separation of Sister Chromatids / chromosome / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / actin cytoskeleton / Processing of DNA double-strand break ends
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 / Kinetochore complex Sim4 subunit Fta1 / 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 / Kinetochore complex Sim4 subunit Fta1 / Centromere protein R / Centromere protein Q / Centromere protein U / Centromere protein P / Centromere protein H / Kinetochore component, CENP-R / CENP-Q, a CENPA-CAD centromere complex subunit / CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P / CENP-A nucleosome associated complex (NAC) subunit / Centromere protein H, C-terminal / Centromere protein Cenp-M / Centromere protein Cenp-K / Centromere protein H (CENP-H) / Centromere protein M (CENP-M) / Centromere-associated protein K / Centromere protein I / Mis6 / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / : / Centromere protein O / Cenp-O kinetochore centromere component / Kinetochore assembly subunit CENP-C, N-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like / RmlC-like cupin domain superfamily / CENP-T/Histone H4, histone fold / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Centromere kinetochore component CENP-T histone fold / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / RmlC-like jelly roll fold / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Centromere protein X / Histone H3-like centromeric protein A / Arachidonate 15-lipoxygenase / Histone H2B type 1-C/E/F/G/I / Centromere protein C / Centromere protein R / Centromere protein W ...DNA / DNA (> 10) / DNA (> 100) / Centromere protein X / Histone H3-like centromeric protein A / Arachidonate 15-lipoxygenase / Histone H2B type 1-C/E/F/G/I / Centromere protein C / Centromere protein R / Centromere protein W / Centromere protein P / Centromere protein U / Centromere protein Q / Centromere protein L / Centromere protein S / Centromere protein I / Histone H2A type 1-C / 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: 12 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 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 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

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Assembly

Deposited unit
H: Centromere protein H
I: Centromere protein I
K: Centromere protein K
L: Centromere protein L
M: Centromere protein M
N: Centromere protein N
O: Centromere protein O
Q: Centromere protein Q
U: Centromere protein U
P: Centromere protein P
R: Centromere protein R
T: Centromere protein T
W: Centromere protein W
S: Centromere protein S
X: Centromere protein X
i: DNA (171-MER)
J: DNA (171-MER)
A: Histone H3-like centromeric protein A
B: Histone H4
C: Histone H2A type 1-C
D: Histone H2B type 1-C/E/F/G/I
E: Histone H3-like centromeric protein A
F: Histone H4
G: Histone H2A type 1-C
V: Histone H2B type 1-C/E/F/G/I
a: Centromere protein C
b: Centromere protein C


Theoretical massNumber of molelcules
Total (without water)846,69927
Polymers846,69927
Non-polymers00
Water00
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 ... , 16 types, 17 molecules HIKLMNOQUPRTWSXab

#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
#3: 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
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#22: Protein Centromere protein C / CENP-C / Centromere autoantigen C / Centromere protein C 1 / CENP-C 1 / Interphase centromere ...CENP-C / Centromere autoantigen C / Centromere protein C 1 / CENP-C 1 / Interphase centromere complex protein 7


Mass: 61856.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPC, CENPC1, ICEN7 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03188

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DNA chain , 2 types, 2 molecules iJ

#16: DNA chain DNA (171-MER)


Mass: 52725.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#17: DNA chain DNA (171-MER)


Mass: 52822.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein , 4 types, 8 molecules AEBFCGDV

#18: Protein Histone H3-like centromeric protein A / Centromere autoantigen A / Centromere protein A / CENP-A


Mass: 16023.630 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPA / Production host: Escherichia coli (E. coli) / References: UniProt: P49450
#19: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#20: Protein Histone H2A type 1-C / H2A-clustered histone 6 / Histone H2A/l


Mass: 14135.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC6, H2AFL, HIST1H2AC / Production host: Escherichia coli (E. coli) / References: UniProt: Q93077
#21: Protein Histone H2B type 1-C/E/F/G/I / Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone ...Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone H2B.k / H2B/k / Histone H2B.l / H2B/l


Mass: 13937.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK
Production host: Escherichia coli (E. coli) / References: UniProt: P62807

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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: CCAN-CENP-A inner centromere complex / Type: COMPLEX / Entity ID: all / 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: 2600 nm / Nominal defocus min: 1200 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: 12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20549 / Symmetry type: POINT

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