8EVG | pdb_00008evg

162bp CX3CR1 nucleosome (further classified with better nucleosome end)

• PDB DOI: https://doi.org/10.2210/pdb8EVG/pdb
• NAKB: 8EVG
• EM Map EMD-28628: EMDB EMDataResource

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens, Mus musculus, Escherichia coli
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2022-10-20 Released: 2023-11-01 
• Deposition Author(s): Tengfei, L., Ruifang, G., Yawen, B.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of cooperative targeting of the CX3CR1 nucleosome

Tengfei, L., Ruifang, G., Yawen, B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 10-mer - A6B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 267.67 kDa 
• Atom Count: 15,577 
• Modeled Residue Count: 1,506 
• Deposited Residue Count: 1,842 
• 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	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:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, 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
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 2-C	C, G	129	Homo sapiens	Mutation(s): 0  Gene Names: H2AC20, H2AFQ, HIST2H2AC
UniProt & NIH Common Fund Data Resources
Find proteins for Q16777 (Homo sapiens) Explore Q16777  Go to UniProtKB:  Q16777
PHAROS:  Q16777 GTEx:  ENSG00000184260

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 2-E	D, H	126	Homo sapiens	Mutation(s): 0  Gene Names: H2BC21, H2BFQ, HIST2H2BE
UniProt & NIH Common Fund Data Resources
Find proteins for Q16778 (Homo sapiens) Explore Q16778  Go to UniProtKB:  Q16778
PHAROS:  Q16778 GTEx:  ENSG00000184678

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-chain variable fragment	K [auth M], L [auth N]	265	Escherichia coli	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (162-MER)	I	162	Mus musculus

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (162-MER)	J	162	Mus musculus

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-01 
Deposition Author(s): Tengfei, L., Ruifang, G., Yawen, B.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2023-11-01
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Structure summary