8EVJ: CX3CR1 nucleosome bound PU.1 and C/EBPa
CX3CR1 nucleosome bound PU.1 and C/EBPa. Determined by electron microscopy at 4.1 Å resolution. Released 1 Nov 2023.
- Method
- Electron microscopy
- Resolution
- 4.1 Å
- Organisms
- Mus musculus, Homo sapiens, Escherichia coli
- Chains
- 13
- Atoms
- 15,951
- Mol. weight
- 303.63 kDa
- Released
- 1 Nov 2023
Explore 8EVJ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8EVJ contains 45 α-helices and 75 β-strands across 11 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118 | 1 | 2 |
| α-helix | 121-130 | 10 | |
Chain B: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| β-strand | 45 | 1 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 84-92 | 9 | |
| β-strand | 96-97 | 2 | 3 |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| α-helix | 46-73 | 28 | |
| β-strand | 77-78 | 2 | 4 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-101 | 2 | 5 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 4 |
| α-helix | 53-80 | 28 | |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 6 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 7 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 7 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 6 |
| α-helix | 83-93 | 11 | |
| β-strand | 96-97 | 2 | 5 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 8 |
| α-helix | 46-71 | 26 | |
| β-strand | 77-78 | 2 | 9 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-101 | 2 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 9 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 8 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| DNA (167-mer) | J | DNA | 167 | Mus musculus | |
| DNA (167-mer) | I | DNA | 167 | Mus musculus | |
| Histone H3.1 | A, E | protein | 136 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 2-C | C, G | protein | 129 | Homo sapiens | Q16777 (AlphaFold model) |
| Histone H2B type 2-E | D, H | protein | 126 | Homo sapiens | Q16778 (AlphaFold model) |
| ScFv | M, N | protein | 265 | Escherichia coli | |
| Transcription factor PU.1 | O | protein | 285 | Mus musculus | P17433 |
Sequence of entity 1 (J), FASTA
>8EVJ_1 DNA (167-MER) (chains J)
TAGAAAAATAGGAACCCCACATGCCCTGTGTCTGCAAGTACAGAACTAGCCAGACAGACT
GACCTATTTTTGTGAGGGGAATCGGGAAGTATCCATTGCTAAGACTCAGCAATGCTGCAA
CTCTCAGCAACCAGCTGAAGATCAGCAGCCGAGAGGCCCTGCACCTA
Sequence of entity 2 (I), FASTA
>8EVJ_2 DNA (167-MER) (chains I)
TAGGTGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCT
GAGTCTTAGCAATGGATACTTCCCGATTCCCCTCACAAAAATAGGTCAGTCTGTCTGGCT
AGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCTATTTTTCTA
Sequence of entity 3 (A, E), FASTA
>8EVJ_3 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 4 (B, F), FASTA
>8EVJ_4 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 5 (C, G), FASTA
>8EVJ_5 Histone H2A type 2-C (chains C, G)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLT
AEILELAGNAARDNKKCRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK
TESHKAKSK
Sequence of entity 6 (D, H), FASTA
>8EVJ_6 Histone H2B type 2-E (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK
Sequence of entity 7 (M, N), FASTA
>8EVJ_7 ScFv (chains M, N)
MKSSHHHHHHENLYFQSNAMEVQLQQSGPELVEPGTSVKMPCKASGYTFTSYTIQWVKQT
PRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSEDSAVYYCARKS
SRLRSTLDYWGQGTSVTVSSGGGGSGGGGSGGGGSMDIKMTQSPSSMHASLGERVTITCK
ASQDIRSYLSWYQQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTA
TYYCLQHGESPYTFGSGTKLEIKRA
Sequence of entity 8 (O), FASTA
>8EVJ_8 Transcription factor PU.1 (chains O)
MGSSHHHHHHSSGMLQACKMEGFSLTAPPSDDLVTYDSELYQRPMHDYYSFVGSDGESHS
DHYWDFSAHHVHNNEFENFPENHFTELQSVQPPQLQQLYRHMELEQMHVLDTPMVPPHTG
LSHQVSYMPRMCFPYQTLSPAHQQSSDEEEGERQSPPLEVSDGEADGLEPGPGLLHGETG
SKKKIRLYQFLLDLLRSGDMKDSIWWVDKDKGTFQFSSKHKEALAHRWGIQKCNRKKMTY
QKMARALRNYGKTGEVKKVKKKLTYQFSGEVLGRGGLAERRLPPH
Primary citation
Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBP alpha. Lian, T., Guan, R., Zhou, B.R. et al. Nat Struct Mol Biol (2024) 31:633-643. DOI 10.1038/s41594-023-01189-z · PubMed
Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
- 2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
- 5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
- 5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
- 5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
- 4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
- 6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
Browse structure collections
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