7YWX

Structure of the human CCAN CENP-A alpha-satellite complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome.

Yatskevich, S.Muir, K.W.Bellini, D.Zhang, Z.Yang, J.Tischer, T.Predin, M.Dendooven, T.McLaughlin, S.H.Barford, D.

(2022) Science 376: 844-852

  • DOI: https://doi.org/10.1126/science.abn3810
  • Primary Citation of Related Structures:  
    7PB4, 7PB8, 7PII, 7PKN, 7R5R, 7R5S, 7R5V, 7YWX, 7YYH

  • PubMed Abstract: 

    Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A Nuc ) 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 Nuc reconstituted onto α-satellite DNA. CCAN forms edge-on contacts with CENP-A Nuc , 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.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein HA [auth H]247Homo sapiensMutation(s): 0 
Gene Names: CENPHICEN35
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3R5 (Homo sapiens)
Explore Q9H3R5 
Go to UniProtKB:  Q9H3R5
PHAROS:  Q9H3R5
GTEx:  ENSG00000153044 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H3R5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein IB [auth I]756Homo sapiensMutation(s): 0 
Gene Names: CENPIFSHPRH1ICEN19LRPR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92674 (Homo sapiens)
Explore Q92674 
Go to UniProtKB:  Q92674
PHAROS:  Q92674
GTEx:  ENSG00000102384 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92674
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein KC [auth K]269Homo sapiensMutation(s): 0 
Gene Names: CENPKICEN37FKSG14
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BS16 (Homo sapiens)
Explore Q9BS16 
Go to UniProtKB:  Q9BS16
PHAROS:  Q9BS16
GTEx:  ENSG00000123219 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BS16
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein LD [auth L]344Homo sapiensMutation(s): 0 
Gene Names: CENPLC1orf155ICEN33
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N0S6 (Homo sapiens)
Explore Q8N0S6 
Go to UniProtKB:  Q8N0S6
PHAROS:  Q8N0S6
GTEx:  ENSG00000120334 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N0S6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein ME [auth M]180Homo sapiensMutation(s): 0 
Gene Names: CENPMC22orf18ICEN39PANE1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NSP4 (Homo sapiens)
Explore Q9NSP4 
Go to UniProtKB:  Q9NSP4
PHAROS:  Q9NSP4
GTEx:  ENSG00000100162 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NSP4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein NF [auth N]339Homo sapiensMutation(s): 0 
Gene Names: CENPNC16orf60ICEN32BM-309
UniProt & NIH Common Fund Data Resources
Find proteins for Q96H22 (Homo sapiens)
Explore Q96H22 
Go to UniProtKB:  Q96H22
PHAROS:  Q96H22
GTEx:  ENSG00000166451 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96H22
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein OG [auth O]300Homo sapiensMutation(s): 0 
Gene Names: CENPOICEN36MCM21R
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BU64 (Homo sapiens)
Explore Q9BU64 
Go to UniProtKB:  Q9BU64
PHAROS:  Q9BU64
GTEx:  ENSG00000138092 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BU64
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein QH [auth Q]268Homo sapiensMutation(s): 0 
Gene Names: CENPQC6orf139
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L2Z9 (Homo sapiens)
Explore Q7L2Z9 
Go to UniProtKB:  Q7L2Z9
PHAROS:  Q7L2Z9
GTEx:  ENSG00000031691 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7L2Z9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein UI [auth U]418Homo sapiensMutation(s): 0 
Gene Names: CENPUICEN24KLIP1MLF1IPPBIP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q71F23 (Homo sapiens)
Explore Q71F23 
Go to UniProtKB:  Q71F23
PHAROS:  Q71F23
GTEx:  ENSG00000151725 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ71F23
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein PJ [auth P]288Homo sapiensMutation(s): 0 
Gene Names: CENPP
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IPU0 (Homo sapiens)
Explore Q6IPU0 
Go to UniProtKB:  Q6IPU0
PHAROS:  Q6IPU0
GTEx:  ENSG00000188312 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IPU0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein RK [auth R]177Homo sapiensMutation(s): 0 
Gene Names: ITGB3BPCENPRNRIF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q13352 (Homo sapiens)
Explore Q13352 
Go to UniProtKB:  Q13352
PHAROS:  Q13352
GTEx:  ENSG00000142856 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13352
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein TL [auth T]561Homo sapiensMutation(s): 0 
Gene Names: CENPTC16orf56ICEN22
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BT3 (Homo sapiens)
Explore Q96BT3 
Go to UniProtKB:  Q96BT3
PHAROS:  Q96BT3
GTEx:  ENSG00000102901 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96BT3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein WM [auth W]88Homo sapiensMutation(s): 0 
Gene Names: CENPWC6orf173CUG2
UniProt & NIH Common Fund Data Resources
Find proteins for Q5EE01 (Homo sapiens)
Explore Q5EE01 
Go to UniProtKB:  Q5EE01
PHAROS:  Q5EE01
GTEx:  ENSG00000203760 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5EE01
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein SN [auth S]138Homo sapiensMutation(s): 0 
Gene Names: CENPSAPITD1FAAP16MHF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N2Z9 (Homo sapiens)
Explore Q8N2Z9 
Go to UniProtKB:  Q8N2Z9
PHAROS:  Q8N2Z9
GTEx:  ENSG00000175279 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N2Z9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein XO [auth X]81Homo sapiensMutation(s): 0 
Gene Names: CENPXFAAP10MHF2STRA13
UniProt & NIH Common Fund Data Resources
Find proteins for A8MT69 (Homo sapiens)
Explore A8MT69 
Go to UniProtKB:  A8MT69
PHAROS:  A8MT69
GTEx:  ENSG00000169689 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8MT69
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3-like centromeric protein AR [auth A],
V [auth E]
140Homo sapiensMutation(s): 0 
Gene Names: CENPA
UniProt & NIH Common Fund Data Resources
Find proteins for P49450 (Homo sapiens)
Explore P49450 
Go to UniProtKB:  P49450
PHAROS:  P49450
GTEx:  ENSG00000115163 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49450
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4S [auth B],
W [auth F]
103Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62805
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-CT [auth C],
X [auth G]
130Homo sapiensMutation(s): 0 
Gene Names: H2AC6H2AFLHIST1H2AC
UniProt & NIH Common Fund Data Resources
Find proteins for Q93077 (Homo sapiens)
Explore Q93077 
Go to UniProtKB:  Q93077
PHAROS:  Q93077
GTEx:  ENSG00000180573 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93077
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/IU [auth D],
Y [auth V]
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BCH2BFLHIST1H2BEH2BFHHIST1H2BFH2BFGHIST1H2BGH2BFAHIST1H2BIH2BFK
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens)
Explore P62807 
Go to UniProtKB:  P62807
PHAROS:  P62807
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62807
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere protein CAA [auth b],
Z [auth a]
544Homo sapiensMutation(s): 0 
Gene Names: CENPCCENPC1ICEN7
UniProt & NIH Common Fund Data Resources
Find proteins for Q03188 (Homo sapiens)
Explore Q03188 
Go to UniProtKB:  Q03188
PHAROS:  Q03188
GTEx:  ENSG00000145241 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03188
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (171-MER)P [auth i]171Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains LengthOrganismImage
DNA (171-MER)Q [auth J]171Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--
Boehringer Ingelheim Fonds (BIF)Germany--
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2024-07-17
    Changes: Data collection