6BUZ

Cryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 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

Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N.

Chittori, S.Hong, J.Saunders, H.Feng, H.Ghirlando, R.Kelly, A.E.Bai, Y.Subramaniam, S.

(2018) Science 359: 339-343

  • DOI: 10.1126/science.aar2781

  • PubMed Abstract: 
  • Accurate chromosome segregation requires the proper assembly of kinetochore proteins. A key step in this process is the recognition of the histone H3 variant CENP-A in the centromeric nucleosome by the kinetochore protein CENP-N. We report cryo-elect ...

    Accurate chromosome segregation requires the proper assembly of kinetochore proteins. A key step in this process is the recognition of the histone H3 variant CENP-A in the centromeric nucleosome by the kinetochore protein CENP-N. We report cryo-electron microscopy (cryo-EM), biophysical, biochemical, and cell biological studies of the interaction between the CENP-A nucleosome and CENP-N. We show that human CENP-N confers binding specificity through interactions with the L1 loop of CENP-A, stabilized by electrostatic interactions with the nucleosomal DNA. Mutational analyses demonstrate analogous interactions in Xenopus , which are further supported by residue-swapping experiments involving the L1 loop of CENP-A. Our results are consistent with the coevolution of CENP-N and CENP-A and establish the structural basis for recognition of the CENP-A nucleosome to enable kinetochore assembly and centromeric chromatin organization.


    Organizational Affiliation

    Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA.,Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA. baiyaw@mail.nih.gov alexander.kelly@nih.gov ss1@nih.gov.,Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.,Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA. baiyaw@mail.nih.gov alexander.kelly@nih.gov ss1@nih.gov.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3-like centromeric protein A
A, E
160Homo 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: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AB, HIST1H2AE (H2AFM, H2AFA)
Find proteins for P04908 (Homo sapiens)
Go to Gene View: HIST1H2AB HIST1H2AE
Go to UniProtKB:  P04908
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, H
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ (H2BFR)
Find proteins for P06899 (Homo sapiens)
Go to Gene View: HIST1H2BJ
Go to UniProtKB:  P06899
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein, Centromere protein N chimera
N
668Escherichia coli O157:H7Homo sapiens
This entity is chimeric
Mutation(s): 5 
Gene Names: malE, CENPN (C16orf60, ICEN32)
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AEY0
Find proteins for Q96H22 (Homo sapiens)
Go to Gene View: CENPN
Go to UniProtKB:  Q96H22
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (147-MER)I147synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (147-MER)J147synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-10
    Type: Database references
  • Version 1.2: 2018-01-31
    Type: Database references