Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A6B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 200.58 kDa 
• Atom Count: 12471 
• Residue Count: 1053 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

2CV5

Crystal structure of human nucleosome core particle

• DOI: 10.2210/pdb2CV5/pdb
• NDB: PD0676

• Classification: Structural Protein/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-05-31 Released: 2005-06-28 
• Deposition Author(s): Tsunaka, Y., Kajimura, N., Tate, S., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.277 
• R-Value Work: 0.224 

Literature

Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle

Tsunaka, Y., Kajimura, N., Tate, S., Morikawa, K.

(2005) Nucleic Acids Res 33: 3424-3434

• PubMed: 15951514 
• DOI: 10.1093/nar/gki663
• Primary Citation of Related Structures:  
  2CV5


• PubMed Abstract: 
  

Gene expression in eukaryotes depends upon positioning, mobility and packaging of nucleosomes; thus, we need the detailed information of the human nucleosome core particle (NCP) structure, which could clarify chromatin properties. Here, we report the 2.5 A crystal structure of a human NCP. The overall structure is similar to those of other NCPs reported previously. However, the DNA path of human NCP is remarkably different from that taken within other NCPs with an identical DNA sequence. A comparison of the structural parameters between human and Xenopus laevis DNA reveals that the DNA path of human NCP consecutively shifts by 1 bp in the regions of superhelix axis location -5.0 to -2.0 and 5.0 to 7.0. This alteration of the human DNA path is caused predominantly by tight DNA-DNA contacts within the crystal. It is also likely that the conformational change in the human H2B tail induces the local alteration of the DNA path. In human NCP, the region with the altered DNA path lacks Mn2+ ions and the B-factors of the DNA phosphate groups are substantially high. Therefore, in contrast to the histone octamer, the nucleosomal DNA is sufficiently flexible and mobile and can undergo drastic conformational changes, depending upon the environment.

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Organizational Affiliation: 

Department of Structural Biology, Biomolecular Engineering Research Institute 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, 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
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431 GTEx  ENSG00000197409GTEx  ENSG00000197153GTEx  ENSG00000278828GTEx  ENSG00000275714GTEx  ENSG00000273983GTEx  ENSG00000274750GTEx  ENSG00000275379GTEx  ENSG00000277775

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, 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
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805 GTEx  ENSG00000274618GTEx  ENSG00000197238GTEx  ENSG00000197837GTEx  ENSG00000158406GTEx  ENSG00000278705GTEx  ENSG00000197061GTEx  ENSG00000270882GTEx  ENSG00000270276GTEx  ENSG00000273542GTEx  ENSG00000277157GTEx  ENSG00000276966GTEx  ENSG00000276180GTEx  ENSG00000278637GTEx  ENSG00000275126

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.a	C, G	130	Homo sapiens	Mutation(s): 0  Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
Find proteins for P04908 (Homo sapiens) Explore P04908  Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS  P04908 GTEx  ENSG00000277075GTEx  ENSG00000278463

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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (146-MER)	I, J	146	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	D, I, J	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	A, C, E, G	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.277 
• R-Value Work: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.564	α = 90
b = 108.37	β = 90
c = 169.425	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-31 
• Released Date: 2005-06-28 
Deposition Author(s): Tsunaka, Y., Kajimura, N., Tate, S., Morikawa, K.

Revision History 

• Version 1.0: 2005-06-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance