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Structure paper

TitleStructural insights into histone binding and nucleosome assembly by chromatin assembly factor-1.
Journal, issue, pagesScience, Vol. 381, Issue 6660, Page eadd8673, Year 2023
Publish dateAug 25, 2023
AuthorsChao-Pei Liu / Zhenyu Yu / Jun Xiong / Jie Hu / Aoqun Song / Dongbo Ding / Cong Yu / Na Yang / Mingzhu Wang / Juan Yu / Peini Hou / Kangning Zeng / Zhenyu Li / Zhuqiang Zhang / Xinzheng Zhang / Wei Li / Zhiguo Zhang / Bing Zhu / Guohong Li / Rui-Ming Xu /
PubMed AbstractChromatin inheritance entails de novo nucleosome assembly after DNA replication by chromatin assembly factor-1 (CAF-1). Yet direct knowledge about CAF-1's histone binding mode and nucleosome assembly ...Chromatin inheritance entails de novo nucleosome assembly after DNA replication by chromatin assembly factor-1 (CAF-1). Yet direct knowledge about CAF-1's histone binding mode and nucleosome assembly process is lacking. In this work, we report the crystal structure of human CAF-1 in the absence of histones and the cryo-electron microscopy structure of CAF-1 in complex with histones H3 and H4. One histone H3-H4 heterodimer is bound by one CAF-1 complex mainly through the p60 subunit and the acidic domain of the p150 subunit. We also observed a dimeric CAF-1-H3-H4 supercomplex in which two H3-H4 heterodimers are poised for tetramer assembly and discovered that CAF-1 facilitates right-handed DNA wrapping of H3-H4 tetramers. These findings signify the involvement of DNA in H3-H4 tetramer formation and suggest a right-handed nucleosome precursor in chromatin replication.
External linksScience / PubMed:37616371 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution3.42 - 6.6 Å
Structure data

EMDB-33625, PDB-7y5u:
Cryo-EM structure of the monomeric human CAF1LC-H3-H4 complex
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-33626, PDB-7y5v:
Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex
Method: EM (single particle) / Resolution: 6.1 Å

EMDB-33627, PDB-7y5w:
Cryo-EM structure of the left-handed Di-tetrasome
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-33630, PDB-7y60:
Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-33631, PDB-7y61:
Cryo-EM structure of the two CAF1LCs bound right-handed Di-tetrasome
Method: EM (single particle) / Resolution: 5.6 Å

EMDB-35660: Composite cryo-EM density map of the dimeric human CAF1-H3-H4 complex
PDB-8iqf: Cryo-EM structure of the dimeric human CAF1-H3-H4 complex
Method: EM (single particle) / Resolution: 4.6 Å

EMDB-35661, PDB-8iqg:
Cryo-EM structure of the monomeric human CAF1-H3-H4 complex
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-35708: Cryo-EM consensus map of the dimeric human CAF1-H3-H4 complex
Method: EM (single particle) / Resolution: 5.9 Å

EMDB-35709: Local refinement cryo-EM map of protomer I of the dimeric human CAF1-H3-H4 complex
Method: EM (single particle) / Resolution: 4.63 Å

EMDB-35710: Local refinement cryo-EM map of protomer II of the dimeric human CAF1-H3-H4 complex
Method: EM (single particle) / Resolution: 4.58 Å

EMDB-36013, PDB-8j6s:
Cryo-EM structure of the single CAF-1 bound right-handed Di-tetrasome
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-36014, PDB-8j6t:
Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome
Method: EM (single particle) / Resolution: 6.6 Å

PDB-7y5k:
Crystal structure of human CAF-1 core complex in spacegroup C2221
Method: X-RAY DIFFRACTION / Resolution: 3.48 Å

PDB-7y5l:
Crystal structure of human CAF-1 core complex in spacegroup C2
Method: X-RAY DIFFRACTION / Resolution: 3.42 Å

PDB-7y5o:
Crystal structure of human CAF-1 core complex in spacegroup P21
Method: X-RAY DIFFRACTION / Resolution: 3.57 Å

Chemicals

ChemComp-GOL:
GLYCEROL

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsREPLICATION / Histone chaperone / Chromatin assembly factor / DNA BINDING PROTEIN/DNA / Left-handed / Di-tetrasome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex / REPLICATION/DNA / REPLICATION-DNA COMPLEX

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