6SEF

Class2C : CENP-A nucleosome in complex with CENP-C central region


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail.

Ali-Ahmad, A.Bilokapic, S.Schafer, I.B.Halic, M.Sekulic, N.

(2019) Embo Rep. 20: e48913-e48913

  • DOI: 10.15252/embr.201948913
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is considered to be a central organizer of the CCAN. We prov ...

    Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is considered to be a central organizer of the CCAN. We provide new molecular insights into the structure of human CENP-A nucleosomes, in isolation and in complex with the CENP-C central region (CENP-C CR ), the main CENP-A binding module of human CENP-C. We establish that the short αN helix of CENP-A promotes DNA flexibility at the nucleosome ends, independently of the sequence it wraps. Furthermore, we show that, in vitro, two regions of human CENP-C (CENP-C CR and CENP-C motif ) both bind exclusively to the CENP-A nucleosome. We find CENP-C CR to bind with high affinity due to an extended hydrophobic area made up of CENP-A V 532 and CENP-A V 533 . Importantly, we identify two key conformational changes within the CENP-A nucleosome upon CENP-C binding. First, the loose DNA wrapping of CENP-A nucleosomes is further exacerbated, through destabilization of the H2A C-terminal tail. Second, CENP-C CR rigidifies the N-terminal tail of H4 in the conformation favoring H4 K20 monomethylation, essential for a functional centromere.


    Organizational Affiliation

    Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.,Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Munich, Germany.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Chemistry, University of Oslo, Oslo, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3-like centromeric protein A
A, E
140Homo sapiensMutation(s): 0 
Gene Names: CENPA
Find proteins for P49450 (Homo sapiens)
Go to Gene View: CENPA
Go to UniProtKB:  P49450
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
103Homo sapiensMutation(s): 0 
Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 2-A
C, G
130Homo sapiensMutation(s): 0 
Gene Names: HIST2H2AA3, HIST2H2AA4 (H2AFO, HIST2H2AA)
Find proteins for Q6FI13 (Homo sapiens)
Go to Gene View: HIST2H2AA3 HIST2H2AA4
Go to UniProtKB:  Q6FI13
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-C/E/F/G/I
D, H
126Homo sapiensMutation(s): 0 
Gene Names: H2BC4, H2BC6, H2BC7, H2BC8, H2BC10 (H2BFL, HIST1H2BC, H2BFH, HIST1H2BE, H2BFG, HIST1H2BF, H2BFA, HIST1H2BG, H2BFK, HIST1H2BI)
Find proteins for P62807 (Homo sapiens)
Go to UniProtKB:  P62807
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Centromere protein C
V
124Homo sapiensMutation(s): 0 
Gene Names: CENPC (CENPC1, ICEN7)
Find proteins for Q03188 (Homo sapiens)
Go to Gene View: CENPC
Go to UniProtKB:  Q03188
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (145-MER)I145synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (145-MER)J145synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway263195
European Research CouncilGermanyERC-smallRNAhet-309584

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-09-11
    Type: Data collection, Database references
  • Version 1.2: 2019-10-16
    Type: Data collection, Database references
  • Version 1.3: 2019-10-23
    Type: Author supporting evidence, Data collection
  • Version 1.4: 2019-11-06
    Type: Data collection, Refinement description