6C0W

Cryo-EM structure of human kinetochore protein CENP-N with the centromeric nucleosome containing CENP-A

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Decoding the centromeric nucleosome through CENP-N.

Pentakota, S., Zhou, K., Smith, C., Maffini, S., Petrovic, A., Morgan, G.P., Weir, J.R., Vetter, I.R., Musacchio, A., Luger, K.

(2017) Elife 6

  • DOI: 10.7554/eLife.33442
  • Primary Citation of Related Structures:  
    6C0W, 6EQT

  • PubMed Abstract: 

    • Centromere protein (CENP) A, a histone H3 variant, is a key epigenetic determinant of chromosome domains known as centromeres. Centromeres nucleate kinetochores, multi-subunit complexes that capture spindle microtubules to promote chromosome segregation during mitosis ...

    Centromere protein (CENP) A, a histone H3 variant, is a key epigenetic determinant of chromosome domains known as centromeres. Centromeres nucleate kinetochores, multi-subunit complexes that capture spindle microtubules to promote chromosome segregation during mitosis. Two kinetochore proteins, CENP-C and CENP-N, recognize CENP-A in the context of a rare CENP-A nucleosome. Here, we reveal the structural basis for the exquisite selectivity of CENP-N for centromeres. CENP-N uses charge and space complementarity to decode the L1 loop that is unique to CENP-A. It also engages in extensive interactions with a 15-base pair segment of the distorted nucleosomal DNA double helix, in a position predicted to exclude chromatin remodelling enzymes. Besides CENP-A, stable centromere recruitment of CENP-N requires a coincident interaction with a newly identified binding motif on nucleosome-bound CENP-C. Collectively, our studies clarify how CENP-N and CENP-C decode and stabilize the non-canonical CENP-A nucleosome to enforce epigenetic centromere specification and kinetochore assembly.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, Maryland, United States.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3-like centromeric protein AA, E140Homo sapiensMutation(s): 0 
Gene Names: CENPA
UniProt & NIH Common Fund Data Resources
Find proteins for P49450 (Homo sapiens)
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Go to UniProtKB:  P49450
PHAROS:  P49450
GTEx:  ENSG00000115163
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F102Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
GTEx:  ENSG00000274618ENSG00000197238ENSG00000197837ENSG00000158406ENSG00000278705ENSG00000197061ENSG00000270882ENSG00000270276ENSG00000273542ENSG00000277157ENSG00000276966ENSG00000276180ENSG00000278637ENSG00000275126
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AC, H2AFL, H2AC6
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Find proteins for Q93077 (Homo sapiens)
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PHAROS:  Q93077
GTEx:  ENSG00000180573
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BD, H126Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62807 (Homo sapiens)
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PHAROS:  P62807
GTEx:  ENSG00000180596ENSG00000277224ENSG00000278588ENSG00000273802ENSG00000274290
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Centromere protein NK295Homo sapiensMutation(s): 1 
Gene Names: CENPN, C16orf60, ICEN32, BM-309
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Find proteins for Q96H22 (Homo sapiens)
Explore Q96H22 
Go to UniProtKB:  Q96H22
PHAROS:  Q96H22
GTEx:  ENSG00000166451
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
147 mer DNAI147Escherichia coli str. 'clone D i2
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Entity ID: 6
MoleculeChainsLengthOrganismImage
147 mer DNAJ147Escherichia coli str. 'clone D i2
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM067777
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Author supporting evidence