6O1D

Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA

  • Classification: NUCLEAR PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-02-19 Released: 2019-05-22 
  • Deposition Author(s): Zhou, B.-R.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment.

Zhou, B.R.Yadav, K.N.S.Borgnia, M.Hong, J.Cao, B.Olins, A.L.Olins, D.E.Bai, Y.Zhang, P.

(2019) Nat Commun 10: 2301-2301

  • DOI: https://doi.org/10.1038/s41467-019-10247-4
  • Primary Citation of Related Structures:  
    6DZT, 6E0C, 6E0P, 6O1D

  • PubMed Abstract: 

    Genomic DNA in eukaryotes is organized into chromatin through association with core histones to form nucleosomes, each distinguished by their DNA sequences and histone variants. Here, we used a single-chain antibody fragment (scFv) derived from the anti-nucleosome antibody mAb PL2-6 to stabilize human CENP-A nucleosome containing a native α-satellite DNA and solved its structure by the cryo-electron microscopy (cryo-EM) to 2.6 Å resolution. In comparison, the corresponding cryo-EM structure of the free CENP-A nucleosome could only reach 3.4 Å resolution. We find that scFv binds to a conserved acidic patch on the histone H2A-H2B dimer without perturbing the nucleosome structure. Our results provide an atomic resolution cryo-EM structure of a nucleosome and insight into the structure and function of the CENP-A nucleosome. The scFv approach is applicable to the structural determination of other native-like nucleosomes with distinct DNA sequences.


  • Organizational Affiliation

    Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3-like centromeric protein A
A, E
158Homo 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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49450
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
PHAROS:  P62805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62805
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFA
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
PHAROS:  P04908
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04908
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFR
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
PHAROS:  P06899
GTEx:  ENSG00000124635 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06899
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (145-MER)145Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (145-MER)145Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0 beta2
MODEL REFINEMENTPHENIX1.13-2998

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2019-05-22 
  • Deposition Author(s): Zhou, B.-R.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United Statesthe intramural research program

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-18
    Changes: Other
  • Version 1.5: 2024-03-20
    Changes: Data collection, Database references, Refinement description