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TitleAtomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment.
Journal, issue, pagesNat Commun, Vol. 10, Issue 1, Page 2301, Year 2019
Publish dateMay 24, 2019
AuthorsBing-Rui Zhou / K N Sathish Yadav / Mario Borgnia / Jingjun Hong / Baohua Cao / Ada L Olins / Donald E Olins / Yawen Bai / Ping Zhang /
PubMed AbstractGenomic 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 ...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.
External linksNat Commun / PubMed:31127102 / PubMed Central
MethodsEM (single particle)
Resolution2.6 - 3.395 Å
Structure data

0586

6o1d

EMDB-0586, PDB-6o1d:
Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA
Method: EM (single particle) / Resolution: 3.395 Å

8938

6dzt

EMDB-8938, PDB-6dzt:
Cryo-EM structure of nucleosome in complex with a single chain antibody fragment
Method: EM (single particle) / Resolution: 2.99 Å

8945

6e0c

EMDB-8945, PDB-6e0c:
Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain antibody fragment
Method: EM (single particle) / Resolution: 2.63 Å

8949

6e0p

EMDB-8949, PDB-6e0p:
Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex with a single chain antibody fragment
Method: EM (single particle) / Resolution: 2.6 Å

Source
  • homo sapiens (human)
  • drosophila melanogaster (fruit fly)
  • mus musculus (house mouse)
  • escherichia coli (E. coli)
KeywordsNUCLEAR PROTEIN / Nucleosome / Single chain antibody / charge-charge interaction / acidic patch. / CENP-A / Centromere / Widom's 601 DNA / anti-nucleosome antibody / acidic patch / Native alpha satellite DNA

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