8EVG: 162bp CX3CR1 nucleosome

162bp CX3CR1 nucleosome (further classified with better nucleosome end). Determined by electron microscopy at 2.75 Å resolution. Released 1 Nov 2023.

Method: Electron microscopy
Resolution: 2.75 Å
Organisms: Homo sapiens, Mus musculus, Escherichia coli
Chains: 12
Atoms: 15,577
Mol. weight: 267.67 kDa
Released: 1 Nov 2023

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

Secondary structure: helices and β-sheets

8EVG contains 42 α-helices and 72 β-strands across 10 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	64-75	12
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

Chains C and G: 6 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	47-72	26
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	3

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	64-75	12
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	26-28	3
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	81	1	7
α-helix	83-91	9
β-strand	96-98	3	6

Chain M: 2 helices, 25 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
β-strand	87	1	13
β-strand	90-95	6	13
β-strand	100-105	6	13
β-strand	114-122	9	12
β-strand	131-132	2	12
β-strand	136-140	5	12
β-strand	168-171	4	14
β-strand	177-180	4	15
β-strand	187	1	16
β-strand	191-196	6	14
β-strand	203-207	5	14
β-strand	211-212	2	14
β-strand	220-225	6	15
β-strand	226	1	16
β-strand	228-233	6	15
α-helix	238-240	3
β-strand	243-248	6	14
β-strand	255-256	2	14
β-strand	261-264	4	14

Chain N: 2 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	17
β-strand	32-34	3	18
β-strand	40-43	4	19
β-strand	46-47	2	17
α-helix	51-53	3
β-strand	54-62	9	18
β-strand	66-74	9	18
β-strand	79-82	4	18
β-strand	87	1	19
β-strand	90-95	6	19
β-strand	100-105	6	19
α-helix	110-112	3
β-strand	114-122	9	18
β-strand	131-132	2	18
β-strand	136-140	5	18
β-strand	163-164	2	20
β-strand	168-171	4	21
β-strand	177-180	4	22
β-strand	181-182	2	20
β-strand	187	1	23
β-strand	191-196	6	21
β-strand	203-207	5	21
β-strand	211-212	2	21
β-strand	220-225	6	22
β-strand	226	1	23
β-strand	228-233	6	22
β-strand	243-248	6	21
β-strand	255-256	2	21
β-strand	261-264	4	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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)
DNA (162-mer)	I	DNA	162	Mus musculus
DNA (162-mer)	J	DNA	162	Mus musculus
Single-chain variable fragment	M, N	protein	265	Escherichia coli

Sequence of entity 1 (A, E), FASTA

>8EVG_1 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>8EVG_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>8EVG_3 Histone H2A type 2-C (chains C, G)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK
TESHKAKSK

Sequence of entity 4 (D, H), FASTA

>8EVG_4 Histone H2B type 2-E (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK

Sequence of entity 5 (I), FASTA

>8EVG_5 DNA (162-MER) (chains I)
TAGGTGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCT
GAGTCTTAGCAATGGATACTTCCCGATTCCCCTCACAAAAATAGGTCAGTCTGTCTGGCT
AGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCTATTT

Sequence of entity 6 (J), FASTA

>8EVG_6 DNA (162-MER) (chains J)
AAATAGGAACCCCACATGCCCTGTGTCTGCAAGTACAGAACTAGCCAGACAGACTGACCT
ATTTTTGTGAGGGGAATCGGGAAGTATCCATTGCTAAGACTCAGCAATGCTGCAACTCTC
AGCAACCAGCTGAAGATCAGCAGCCGAGAGGCCCTGCACCTA

Sequence of entity 7 (M, N), FASTA

>8EVG_7 Single-chain variable fragment (chains M, N)
MKSSHHHHHHENLYFQSNAMEVQLQQSGPELVEPGTSVKMPCKASGYTFTSYTIQWVKQT
PRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSEDSAVYYCARKS
SRLRSTLDYWGQGTSVTVSSGGGGSGGGGSGGGGSMDIKMTQSPSSMHASLGERVTITCK
ASQDIRSYLSWYQQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTA
TYYCLQHGESPYTFGSGTKLEIKRA

Primary citation

Structural basis of cooperative targeting of the CX3CR1 nucleosome. Tengfei, L., Ruifang, G., Yawen, B. To be published.

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

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