6SEE

Class2A : CENP-A nucleosome in complex with CENP-C central region


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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:  
    6SEE, 6SEG, 6SEF, 6SE0, 6SE6

  • 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

    Department of Chemistry, University of Oslo, Oslo, Norway.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3-like centromeric protein AAE140Homo sapiensMutation(s): 0 
Gene Names: CENPA
Find proteins for P49450 (Homo sapiens)
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Go to UniProtKB:  P49450
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PHAROS  P49450
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF103Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
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PHAROS  P62805
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 2-ACG130Homo sapiensMutation(s): 0 
Gene Names: HIST2H2AA3H2AFOHIST2H2AAHIST2H2AA4H2AC18H2AC19
Find proteins for Q6FI13 (Homo sapiens)
Explore Q6FI13 
Go to UniProtKB:  Q6FI13
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PHAROS  Q6FI13
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/IDH126Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62807 (Homo sapiens)
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PHAROS  P62807
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Centromere protein CV124Homo sapiensMutation(s): 0 
Gene Names: CENPCCENPC1ICEN7
Find proteins for Q03188 (Homo sapiens)
Explore Q03188 
Go to UniProtKB:  Q03188
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PHAROS  Q03188
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (145-MER)I145synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)J145synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-23
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-11-06
    Changes: Data collection, Refinement description