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:  

  • 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

    Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.,Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA. ping.zhang@nih.gov.,Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME, 04103, USA.,Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA. BaiYaw@mail.nih.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3
A, E
136Drosophila melanogasterMutation(s): 0 
Gene Names: His3, His3:CG31613, His3:CG33803, His3:CG33806, His3:CG33809, His3:CG33812, His3:CG33815, His3:CG33818, His3:CG33821, His3:CG33824, His3:CG33827, His3:CG33830, His3:CG33833, His3:CG33836, His3:CG33839, His3:CG33842, His3:CG33845, His3:CG33848, His3:CG33851, His3:CG33854, His3:CG33857, His3:CG33860, His3:CG33863, His3:CG33866
Find proteins for P02299 (Drosophila melanogaster)
Go to UniProtKB:  P02299
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
104Drosophila melanogasterMutation(s): 0 
Gene Names: His4, His4r, His4:CG31611, His4:CG33869, His4:CG33871, His4:CG33873, His4:CG33875, His4:CG33877, His4:CG33879, His4:CG33881, His4:CG33883, His4:CG33885, His4:CG33887, His4:CG33889, His4:CG33891, His4:CG33893, His4:CG33895, His4:CG33897, His4:CG33899, His4:CG33901, His4:CG33903, His4:CG33905, His4:CG33907, His4:CG33909 (H4, H4r)
Find proteins for P84040 (Drosophila melanogaster)
Go to UniProtKB:  P84040
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
124Drosophila melanogasterMutation(s): 0 
Gene Names: His2A, His2A:CG31618, His2A:CG33808, His2A:CG33814, His2A:CG33817, His2A:CG33820, His2A:CG33823, His2A:CG33826, His2A:CG33829, His2A:CG33832, His2A:CG33835, His2A:CG33838, His2A:CG33841, His2A:CG33844, His2A:CG33847, His2A:CG33850, His2A:CG33862, His2A:CG33865 (H2a)
Find proteins for P84051 (Drosophila melanogaster)
Go to UniProtKB:  P84051
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, H
124Drosophila melanogasterMutation(s): 0 
Gene Names: His2B, His2B:CG17949, His2B:CG33868, His2B:CG33870, His2B:CG33872, His2B:CG33874, His2B:CG33876, His2B:CG33878, His2B:CG33880, His2B:CG33882, His2B:CG33884, His2B:CG33886, His2B:CG33888, His2B:CG33890, His2B:CG33892, His2B:CG33894, His2B:CG33896, His2B:CG33898, His2B:CG33900, His2B:CG33902, His2B:CG33904, His2B:CG33906, His2B:CG33908, His2B:CG33910
Find proteins for P02283 (Drosophila melanogaster)
Go to UniProtKB:  P02283
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
scFv
M, N
265N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (147-MER)I147Escherichia coli
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (147-MER)J147Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
phenix.real_space_refinerefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references
  • Version 1.2: 2019-06-19
    Type: Data collection, Database references
  • Version 1.3: 2019-11-20
    Type: Database references
  • Version 1.4: 2019-12-04
    Type: Author supporting evidence
  • Version 1.5: 2019-12-18
    Type: Other