› 8evj

Electron Microscopy
4.1Å resolution

CX3CR1 nucleosome bound PU.1 and C/EBPa

Released:
DOI: 10.2210/pdb8evj/pdb
PDB entry 8evj coloured by chain, front view.
PDB entry 8evj coloured by chain, side view.
PDB entry 8evj coloured by chain, top view.
Source organisms:
Primary publication:
Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBPα.
Lian T, Guan R, Zhou BR, Bai Y
Nat Struct Mol Biol (2024)
PMID: 38267599
Related structures: EMD-28631

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tridecamer (preferred)
PDBe Complex ID:
PDB-CPX-233829 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
Histone H3.1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P68431 (Residues: 1-136; Coverage: 100%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 1-103; Coverage: 100%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 2-C Chains: C, G
Molecule details ›
Chains: C, G
Length: 129 amino acids
Theoretical weight: 14.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q16777 (Residues: 1-129; Coverage: 100%)
Gene names: H2AC20, H2AFQ, HIST2H2AC
Sequence domains:
Histone H2B type 2-E Chains: D, H
Molecule details ›
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q16778 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC21, H2BFQ, HIST2H2BE
Sequence domains: Core histone H2A/H2B/H3/H4
ScFv Chains: M, N
Molecule details ›
Chains: M, N
Length: 265 amino acids
Theoretical weight: 29.03 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
Transcription factor PU.1 Chain: O
Molecule details ›
Chain: O
Length: 285 amino acids
Theoretical weight: 32.87 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P17433 (Residues: 1-272; Coverage: 100%)
Gene names: Sfpi-1, Sfpi1, Spi1
Sequence domains: Ets-domain
DNA (167-MER) Chain: J
Molecule details ›
Chain: J
Length: 167 nucleotides
Theoretical weight: 51.54 KDa
DNA (167-MER) Chain: I
Molecule details ›
Chain: I
Length: 167 nucleotides
Theoretical weight: 51.56 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-28631
Expression system: Escherichia coli

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