4X23: Cenp-C

Crystal structure of cenp-C in complex with the nucleosome core particle. Determined by X-ray diffraction at 3.5 Å resolution. Released 10 Dec 2014.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Homo sapiens, Drosophila melanogaster, Rattus norvegicus
Chains: 24
Atoms: 23,974
Mol. weight: 359.94 kDa
Released: 10 Dec 2014

Explore 4X23 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4X23 contains 69 α-helices and 42 β-strands across 18 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-55	11
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

Chains C, M and Q: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
β-strand	41-42	2	4
α-helix	46-70	25
β-strand	76-77	2	5
α-helix	79-86	8
α-helix	90-95	6
β-strand	100-101	2	6
α-helix	112-114	3

Chain D: 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	102-117	16

Chains E, K and O: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-55	11
α-helix	64-78	15
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chains F, L and P: 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	80-81	2	7
α-helix	83-91	9
β-strand	97-98	2	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
β-strand	41-42	2	9
α-helix	46-70	25
β-strand	76-77	2	10
α-helix	79-86	8
α-helix	90-95	6
β-strand	99-101	3	3
α-helix	112-114	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	103-120	18

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 (147-mer)	I, S	DNA	147	Homo sapiens
DNA (147-mer)	J, T	DNA	147	Homo sapiens
Histone H3	A, E, K, O	protein	98	Drosophila melanogaster	P02299 (AlphaFold model)
Histone H4	B, F, L, P	protein	79	Drosophila melanogaster	P84040 (AlphaFold model)
Histone H2A	C, G, M, Q	protein	102	Drosophila melanogaster	P84051 (AlphaFold model)
Histone H2B	D, H, N, R	protein	90	Drosophila melanogaster	P02283 (AlphaFold model)
Cenp-C	U, V, W, X	protein	25	Rattus norvegicus	Q66LH7

Sequence of entity 1 (I, S), FASTA

>4X23_1 DNA (147-MER) (chains I, S)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT

Sequence of entity 2 (J, T), FASTA

>4X23_2 DNA (147-MER) (chains J, T)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT

Sequence of entity 3 (A, E, K, O), FASTA

>4X23_3 Histone H3 (chains A, E, K, O)
RYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAY
LVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGIEGGL

Sequence of entity 4 (B, F, L, P), FASTA

>4X23_4 Histone H4 (chains B, F, L, P)
DNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTA
MDVVYALKRQGRTLYGFGG

Sequence of entity 5 (C, G, M, Q), FASTA

>4X23_5 Histone H2A (chains C, G, M, Q)
SRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK
TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLP

Sequence of entity 6 (D, H, N, R), FASTA

>4X23_6 Histone H2B (chains D, H, N, R)
ESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREI
QTAVRLLLPGELAKHAVSEGTKAVTKYTSS

Sequence of entity 7 (U, V, W, X), FASTA

>4X23_7 CENP-C (chains U, V, W, X)
PNVRRSNRIRLKPLEYWRGERIDYQ

Primary citation

A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C. Kato, H., Jiang, J.S., Zhou, B.R. et al. Science (2013) 340:1110-1113. DOI 10.1126/science.1235532 · PubMed

Other PDB entries of the same protein (UniProt P02299 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6AT0 1.28 Å, Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone…
6MHA 1.5 Å, dHP1 Chromodomain Y24W variant bound to histone H3 peptide containing trimethyllysine
6ASZ 1.52 Å, Chromodomain HP1 with Y24F mutation bound to histone H3 peptide containing trimethyl…
7VRF 1.7 Å, Crystal structure of Oxpecker chromodomain in complex with H3K9me3
1KNA 2.1 Å, Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9.
9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
2NQB 2.3 Å, Drosophila Nucleosome Structure
9ZQC 2.37 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2
1KNE 2.4 Å, Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9
2PYO 2.43 Å, Drosophila nucleosome core
8UX1 2.5 Å, Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle
4QUF 2.5 Å, crystal structure of chromodomain of Rhino with H3K9me3

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