7R5R | pdb_00007r5r

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7R5R

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 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.

Macromolecule Content 

  • Total Structure Weight: 339.98 kDa 
  • Atom Count: 11,625 
  • Modeled Residue Count: 1,045 
  • Deposited Residue Count: 2,426 
  • Unique protein chains: 5
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3-like centromeric protein A
A, 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 
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UniProt GroupP49450
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4
B, 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
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UniProt GroupP62805
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A type 1-C
C, 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 
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UniProt GroupQ93077
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/I
D, H
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
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UniProt GroupP62807
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein C
K, L
543Homo 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 
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UniProt GroupQ03188
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (171-MER)171Homo sapiens
Sequence Annotations
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Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (171-MER)171Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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: 2022-04-27
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2024-07-17
    Changes: Data collection