6DZT

Cryo-EM structure of nucleosome in complex with a single chain antibody fragment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 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: 10.1038/s41467-019-10247-4
  • Primary Citation of Related Structures:  
    6O1D, 6DZT, 6E0P, 6E0C

  • 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 a ...

    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

    Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA. ping.zhang@nih.gov.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3AE136Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P02299 (Drosophila melanogaster)
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Go to UniProtKB:  P02299
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF104Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P84040 (Drosophila melanogaster)
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Go to UniProtKB:  P84040
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2ACG124Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P84051 (Drosophila melanogaster)
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Go to UniProtKB:  P84051
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2BDH124Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for P02283 (Drosophila melanogaster)
Explore P02283 
Go to UniProtKB:  P02283
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
scFvMN265Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (147-MER)I147Escherichia coli
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (147-MER)J147Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesIntramural Research Program

Revision History 

  • 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: 2019-11-20
    Changes: Database references
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2019-12-18
    Changes: Other