6M4H

Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2

• PDB DOI:  https://doi.org/10.2210/pdb6M4H/pdb
• EM Map EMD-30078: EMDB EMDataResource
• NAKB: 6M4H

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-03-07 Released: 2020-09-23 
• Deposition Author(s): Zhou, M., Dai, L.C., Li, C.M., Shi, L.X., Huang, Y., Guo, Z.Q.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of nucleosome dynamics modulation by histone variants H2A.B and H2A.Z.2.2.

Zhou, M., Dai, L., Li, C., Shi, L., Huang, Y., Guo, Z., Wu, F., Zhu, P., Zhou, Z.

(2021) EMBO J 40: e105907-e105907

• PubMed: 33073403 
• DOI: https://doi.org/10.15252/embj.2020105907
• Primary Citation of Related Structures:  
  6M4D, 6M4G, 6M4H


• PubMed Abstract: 
  

Nucleosomes are dynamic entities with wide-ranging compositional variations. Human histone variants H2A.B and H2A.Z.2.2 play critical roles in multiple biological processes by forming unstable nucleosomes and open chromatin structures, but how H2A.B and H2A.Z.2.2 confer these dynamic features to nucleosomes remains unclear. Here, we report cryo-EM structures of nucleosome core particles containing human H2A.B (H2A.B-NCP) at atomic resolution, identifying large-scale structural rearrangements in the histone octamer in H2A.B-NCP. H2A.B-NCP compacts approximately 103 bp of DNA wrapping around the core histones in approximately 1.2 left-handed superhelical turns, in sharp contrast to canonical nucleosome encompassing approximately 1.7 turns of DNA. Micrococcal nuclease digestion assay reveals that nineteen H2A.B-specific residues, including a ROF ("regulating-octamer-folding") sequence of six consecutive residues, are responsible for loosening of H2A.B-NCPs. Unlike H2A.B-NCP, the H2A.Z.2.2-containing nucleosome (Z.2.2-NCP) adopts a less-extended structure and compacts around 125 bp of DNA. Further investigation uncovers a crucial role for the H2A.Z.2.2-specific ROF in both H2A.Z.2.2-NCP opening and SWR1-dependent histone replacement. Taken together, these first high-resolution structure of unstable nucleosomes induced by histone H2A variants elucidate specific functions of H2A.B and H2A.Z.2.2 in enhancing chromatin dynamics.

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Organizational Affiliation: 

University of Chinese Academy of Sciences, Beijing, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A7B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 197.78 kDa 
• Atom Count: 9,420 
• Modelled Residue Count: 862 
• Deposited Residue Count: 1,254 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	C [auth A], G [auth E]	136	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ, H3C1, H3C2, H3C3, H3FC HIST1H3C, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D [auth B], H [auth F]	103	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A-Bbd type 2/3	E [auth C], I [auth G]	115	Homo sapiens	Mutation(s): 0  Gene Names: H2AB2, H2AFB2, H2AB3, H2ABBD, H2AFB, H2AFB3
UniProt
Find proteins for P0C5Z0 (Homo sapiens) Explore P0C5Z0  Go to UniProtKB:  P0C5Z0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 2-E	F [auth D], J [auth H]	126	Homo sapiens	Mutation(s): 0  Gene Names: HIST2H2BE, H2BFQ, H2BC21
UniProt & NIH Common Fund Data Resources
Find proteins for Q16778 (Homo sapiens) Explore Q16778  Go to UniProtKB:  Q16778
PHAROS:  Q16778

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (103-MER)	A [auth I]	147	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (103-MER)	B [auth J]	147	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Zhou, M., Dai, L.C., Li, C.M., Shi, L.X., Huang, Y., Guo, Z.Q.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--

Revision History  

• Version 1.0: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2021-04-07
  Changes: Database references