6DZT image
Deposition Date 2018-07-05
Release Date 2019-05-22
Last Version Date 2024-10-23
Entry Detail
PDB ID:
6DZT
Keywords:
NUCLEAR PROTEIN
Title:
Cryo-EM structure of nucleosome in complex with a single chain antibody fragment
Biological Source:
Source Organism:
Drosophila melanogaster (Taxon ID: 7227)
Mus musculus (Taxon ID: 10090)
Escherichia coli (Taxon ID: 562)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.99 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6DZT validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3
Gene (Uniprot):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
Chain IDs:A, E
Chain Length:136
Number of Molecules:2
Biological Source:Drosophila melanogaster
UniProt ID:P02299 Pfam ID:PF00125
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):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
Chain IDs:B, F
Chain Length:104
Number of Molecules:2
Biological Source:Drosophila melanogaster
UniProt ID:P84040 Pfam ID:PF15511
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A
Gene (Uniprot):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
Chain IDs:C, G
Chain Length:124
Number of Molecules:2
Biological Source:Drosophila melanogaster
UniProt ID:P84051 Pfam ID:PF00125, PF16211
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B
Gene (Uniprot):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
Chain IDs:D, H
Chain Length:124
Number of Molecules:2
Biological Source:Drosophila melanogaster
UniProt ID:P02283 Pfam ID:PF00125
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (147-MER)
Chain IDs:I
Chain Length:147
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (147-MER)
Chain IDs:J
Chain Length:147
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:scFv
Chain IDs:K (auth: M), L (auth: N)
Chain Length:265
Number of Molecules:2
Biological Source:Mus musculus
Ligand Molecules
NA
Primary Citation
Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment.
Nat Commun 10 2301 2301 (2019)
PMID: 31127102 DOI: 10.1038/s41467-019-10247-4

Abstact

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.

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Primary Citation of related structures
6DZT