Biological Assembly 1  

 3D View: Structure | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A8B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 242.00 kDa 
• Atom Count: 13801 
• Modelled Residue Count: 1187 
• Deposited Residue Count: 1555 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

7DBP

Linker histone defines structure and self-association behaviour of the 177 bp human chromosome

• DOI: 10.2210/pdb7DBP/pdb
• EMDataResource: EMD-30161

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-10-21 Released: 2020-12-23 
• Deposition Author(s): Wang, S., Vogirala, K.V., Soman, A., Liu, Z.B.
• Funding Organization(s): Ministry of Education (MoE, Singapore)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome.

Wang, S., Vogirala, V.K., Soman, A., Berezhnoy, N.V., Liu, Z.B., Wong, A.S.W., Korolev, N., Su, C.J., Sandin, S., Nordenskiold, L.

(2021) Sci Rep 11: 380-380

• PubMed: 33432055 
• DOI: 10.1038/s41598-020-79654-8
• Primary Citation of Related Structures:  
  7DBP


• PubMed Abstract: 
  

Linker histones play essential roles in the regulation and maintenance of the dynamic chromatin structure of higher eukaryotes. The influence of human histone H1.0 on the nucleosome structure and biophysical properties of the resulting chromatosome were investigated and compared with the 177-bp nucleosome using Cryo-EM and SAXS. The 4.5 Å Cryo-EM chromatosome structure showed that the linker histone binds at the nucleosome dyad interacting with both linker DNA arms but in a tilted manner leaning towards one of the linker sides. The chromatosome is laterally compacted and rigid in the dyad and linker DNA area, in comparison with the nucleosome where linker DNA region is more flexible and displays structural variability. In solution, the chromatosomes appear slightly larger than the nucleosomes, with the volume increase compared to the bound linker histone, according to solution SAXS measurements. SAXS X-ray diffraction characterisation of Mg-precipitated samples showed that the different shapes of the 177 chromatosome enabled the formation of a highly ordered lamello-columnar phase when precipitated by Mg ²⁺ , indicating the influence of linker histone on the nucleosome stacking. The biological significance of linker histone, therefore, may be affected by the change in the polyelectrolyte and DNA conformation properties of the chromatosomes, in comparison to nucleosomes.

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Organizational Affiliation: 

School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr., Singapore, 637551, Singapore. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H1.0	A [auth K]	211	Homo sapiens	Mutation(s): 0  Gene Names: H1-0, H1F0, H1FV
UniProt & NIH Common Fund Data Resources
Find proteins for P07305 (Homo sapiens) Explore P07305  Go to UniProtKB:  P07305
PHAROS:  P07305 GTEx:  ENSG00000189060

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	B [auth A], F [auth E]	136	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409ENSG00000197153ENSG00000278828ENSG00000275714ENSG00000273983ENSG00000274750ENSG00000275379ENSG00000277775

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	C [auth B], G [auth F]	103	Homo sapiens	Mutation(s): 0  Gene Names:  H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618ENSG00000197238ENSG00000197837ENSG00000158406ENSG00000278705ENSG00000197061ENSG00000270882ENSG00000270276ENSG00000273542ENSG00000277157ENSG00000276966ENSG00000276180ENSG00000278637ENSG00000275126

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	D [auth C], H [auth G]	130	Homo sapiens	Mutation(s): 0  Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908  Go to UniProtKB:  P04908
PHAROS:  P04908 GTEx:  ENSG00000277075ENSG00000278463

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-K	E [auth D], I [auth H]	126	Homo sapiens	Mutation(s): 0  Gene Names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens) Explore O60814  Go to UniProtKB:  O60814
PHAROS:  O60814 GTEx:  ENSG00000197903

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (175-MER)	J [auth I]	177	synthetic construct

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (175-MER)	K [auth J]	177	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-10-21 
• Released Date: 2020-12-23 
Deposition Author(s): Wang, S., Vogirala, K.V., Soman, A., Liu, Z.B.

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Funding Organization	Location	Grant Number
Ministry of Education (MoE, Singapore)	Singapore	MOE2012-T3-1-001
Ministry of Education (MoE, Singapore)	Singapore	2014-T1-001-134

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Database references