7XVL | pdb_00007xvl

Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment)

• PDB DOI: https://doi.org/10.2210/pdb7XVL/pdb
• NAKB: 7XVL

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


• Deposited: 2022-05-24 Released: 2023-05-24 
• Deposition Author(s): Adhireksan, Z., Qiuye, B., Lee, P.L., Sharma, D., Padavattan, S., Davey, C.A.
• Funding Organization(s): Ministry of Education (MoE, Singapore)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.51 Å
• R-Value Free: 
  0.280 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.209 (DCC) 

Starting Models: experimental

Literature

Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment)

Adhireksan, Z., Sharma, D., Qiuye, B., Lee, P.L., Padavattan, S., Davey, C.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 17-mer - A4B4C4D4E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 17-mer - A12B4C1 Local Symmetry: Dihedral - D2  (Explore in 3D)
Local Stoichiometry: Hetero 16-mer - A4B4C4D4 

Local Symmetry: Dihedral - D2  (Explore in 3D)
Local Stoichiometry: Hetero 16-mer - A4B4C4D4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 16-mer - A4B4C4D4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 16-mer - A13B3 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 882.38 kDa 
• Atom Count: 52,574 
• Modeled Residue Count: 4,482 
• Deposited Residue Count: 5,571 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E, EA [auth e], IA [auth i], K, O, U, Y	138	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:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F, FA [auth f], JA [auth j], L, P, V, Z	105	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:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	AA [auth a], C, G, GA [auth g], KA [auth k], M, Q, W	132	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:  ENSG00000277075 ENSG00000278463

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	BA [auth b], D, H, HA [auth h], LA [auth l], N, R, X	128	Homo sapiens	Mutation(s): 0  Gene Names: H2BC11, H2BFR, HIST1H2BJ
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899
PHAROS:  P06899 GTEx:  ENSG00000124635

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H1.0	OA [auth o]	195	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: 5
Molecule	Chains	Length	Organism	Image
DNA (169-MER)	CA [auth c], I, MA [auth m], S	169	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (169-MER)	DA [auth d], J, NA [auth n], T	169	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.51 Å
• R-Value Free:  0.280 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.209 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 213.85	α = 90
b = 102.46	β = 100.49
c = 218.289	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Adhireksan, Z., Qiuye, B., Lee, P.L., Sharma, D., Padavattan, S., Davey, C.A.

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Funding Organization	Location	Grant Number
Ministry of Education (MoE, Singapore)	Singapore	MOE2015-T2-2-089
Ministry of Education (MoE, Singapore)	Singapore	MOE2012-T3-1-001

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 2.0: 2024-04-03
  Type: Coordinate replacement
  Reason: Real space R-factor
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary