8EVI: Histone H3.1

CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations. Determined by electron microscopy at 2.64 Å resolution. Released 1 Nov 2023.

Method: Electron microscopy
Resolution: 2.64 Å
Organisms: Mus musculus, Homo sapiens, Escherichia coli
Chains: 13
Atoms: 16,157
Mol. weight: 303.63 kDa
Released: 1 Nov 2023

Explore 8EVI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EVI contains 49 α-helices and 78 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	45-54	10
α-helix	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-91	9
β-strand	96-98	3	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	6

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	102-119	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-78	15
β-strand	84	1	7
α-helix	86-113	28
β-strand	118-119	2	8
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	8
α-helix	50-75	26
β-strand	81	1	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	3

Chain M: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	11
β-strand	32-34	3	12
β-strand	40-43	4	13
β-strand	46-47	2	11
α-helix	51-53	3
β-strand	54-62	9	12
β-strand	66-74	9	12
β-strand	79-82	4	12
α-helix	84-86	3
β-strand	87	1	13
β-strand	90-95	6	13
β-strand	100-105	6	13
α-helix	110-112	3
β-strand	114-122	9	12
β-strand	129-132	4	12
β-strand	136-140	5	12
β-strand	162	1	14
β-strand	168-171	4	15
β-strand	177-180	4	16
β-strand	183	1	14
β-strand	187	1	17
β-strand	191-196	6	15
β-strand	202-207	6	15
β-strand	211-212	2	15
α-helix	213	1
β-strand	220-225	6	16
β-strand	226	1	17
β-strand	228-233	6	16
α-helix	238-240	3
β-strand	242-248	7	15
β-strand	255-256	2	15
β-strand	260-264	5	15

2 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	protein	129	Homo sapiens	Q16777 (AlphaFold model)
Histone H2B type 2-E	D, H	protein	126	Homo sapiens	Q16778 (AlphaFold model)
Histone H2A type 2-C	G	protein	129	Homo sapiens	Q16777 (AlphaFold model)
Single-chain variable fragment	M, N	protein	265	Escherichia coli
Transcription factor PU.1	O	protein	285	Mus musculus	P17433

Sequence of entity 1 (J), FASTA

>8EVI_1 DNA (167-MER) (chains J)
TAGAAAAATAGGAACCCCACATGCCCTGTGTCTGCAAGTACAGAACTAGCCAGACAGACT
GACCTATTTTTGTGAGGGGAATCGGGAAGTATCCATTGCTAAGACTCAGCAATGCTGCAA
CTCTCAGCAACCAGCTGAAGATCAGCAGCCGAGAGGCCCTGCACCTA

Sequence of entity 2 (I), FASTA

>8EVI_2 DNA (167-MER) (chains I)
TAGGTGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCT
GAGTCTTAGCAATGGATACTTCCCGATTCCCCTCACAAAAATAGGTCAGTCTGTCTGGCT
AGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCTATTTTTCTA

Sequence of entity 3 (A, E), FASTA

>8EVI_3 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 4 (B, F), FASTA

>8EVI_4 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (C), FASTA

>8EVI_5 Histone H2A type 2-C (chains C)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLT
AEILELAGNAARDNKKCRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK
TESHKAKSK

Sequence of entity 6 (D, H), FASTA

>8EVI_6 Histone H2B type 2-E (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK

Sequence of entity 7 (G), FASTA

>8EVI_7 Histone H2A type 2-C (chains G)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK
TESHKAKSK

Sequence of entity 8 (M, N), FASTA

>8EVI_8 Single-chain variable fragment (chains M, N)
MKSSHHHHHHENLYFQSNAMEVQLQQSGPELVEPGTSVKMPCKASGYTFTSYTIQWVKQT
PRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSEDSAVYYCARKS
SRLRSTLDYWGQGTSVTVSSGGGGSGGGGSGGGGSMDIKMTQSPSSMHASLGERVTITCK
ASQDIRSYLSWYQQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTA
TYYCLQHGESPYTFGSGTKLEIKRA

Sequence of entity 9 (O), FASTA

>8EVI_9 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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