6C0W: Histone H3-like centromeric protein A

Cryo-EM structure of human kinetochore protein CENP-N with the centromeric nucleosome containing CENP-A. Determined by electron microscopy at 4.0 Å resolution. Released 17 Jan 2018.

Method: Electron microscopy
Resolution: 4.0 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 11
Atoms: 13,122
Mol. weight: 236.49 kDa
Released: 17 Jan 2018

Explore 6C0W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C0W contains 43 α-helices and 25 β-strands across 9 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	48-54	7
α-helix	64-75	12
β-strand	85-86	2	1
α-helix	90-113	24
β-strand	120-121	2	2
α-helix	123-126	4

Chain B: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	33-41	9
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-93	11
β-strand	96-97	2	3

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	28-36	9
α-helix	47-72	26
β-strand	77-78	2	4
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-101	2	5

Chain D: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	4
α-helix	58-66	9
α-helix	69-79	11
α-helix	91-101	11
α-helix	104-122	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	47-54	8
α-helix	64-77	14
β-strand	85-86	2	6
α-helix	88-109	22
α-helix	110-112	3
β-strand	120	1	7
α-helix	123-133	11

Chain F: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45	1	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	17-20	4
α-helix	28-35	8
β-strand	42-43	2	8
α-helix	47-72	26
β-strand	77-78	2	9
α-helix	80-89	10
α-helix	92-96	5
β-strand	100-101	2	3

Chain H: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	9
α-helix	58-66	9
α-helix	69-79	11
β-strand	88-89	2	8
α-helix	91-101	11
α-helix	104-122	19

1 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
Histone H3-like centromeric protein A	A, E	protein	140	Homo sapiens	P49450 (AlphaFold model)
Histone H4	B, F	protein	102	Homo sapiens	P62805 (AlphaFold model)
Histone H2A	C, G	protein	130	Homo sapiens	Q93077 (AlphaFold model)
Histone H2B	D, H	protein	126	Homo sapiens	P62807 (AlphaFold model)
147 mer DNA	I	DNA	147	Escherichia coli
147 mer DNA	J	DNA	147	Escherichia coli
Centromere protein N	K	protein	295	Homo sapiens	Q96H22

Sequence of entity 1 (A, E), FASTA

>6C0W_1 Histone H3-like centromeric protein A (chains A, E)
MGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSRRRQGWLKEIRKLQKSTHL
LIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVT
LFPKDVQLARRIRGLEEGLG

Sequence of entity 2 (B, F), FASTA

>6C0W_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFG

Sequence of entity 3 (C, G), FASTA

>6C0W_3 Histone H2A (chains C, G)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>6C0W_4 Histone H2B (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK

Sequence of entity 5 (I), FASTA

>6C0W_5 147 mer DNA (chains I)
ATCTGAGAATCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT

Sequence of entity 6 (J), FASTA

>6C0W_6 147 mer DNA (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGATTCTCAGAT

Sequence of entity 7 (K), FASTA

>6C0W_7 Centromere protein N (chains K)
MDETVAEFIKRTILKIPMNELTTILKAWDFLSENQLQTVNFRQRKESVVQHLIHLCEEKR
ASISDAALLDIIYMQFHQHQKVWDVFQMSKGPGEDVDLFDMKQFKNSFKKILQRALKNVT
VSFRETEENAVWIRIAWGTQYTKPNQYKPTYVVYYSQTPYAFTSSSMLRRNTPLLGQALT
IASKHHQIVKMDLRSRYLDSLKAIVFKQYNQTFETHNSTTPLQERSLGLDINMDSRIIHE
NIVEKERVQRITQETFGDYPQPQLEFAQYKLETKFKSGLNGSILAEREEHHHHHH

Primary citation

Decoding the centromeric nucleosome through CENP-N. Pentakota, S., Zhou, K., Smith, C. et al. Elife (2017) 6. DOI 10.7554/eLife.33442 · PubMed

Other PDB entries of the same protein (UniProt P49450 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5CVD 1.3 Å, Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide
6KDQ 1.5 Å, Crystal structure of human NRMT1 in complex with alpha-N-monomethylated human CENP-A…
6KDS 1.84 Å, Crystal structure of human NRMT2 in complex with alpha-N-monomethylated human CENP-A…
3NQJ 2.1 Å, Crystal structure of (CENP-A/H4)2 heterotetramer
7R5R 2.44 Å, Structure of the human CCAN CENP-A alpha-satellite complex
3NQU 2.5 Å, Crystal structure of partially trypsinized (CENP-A/H4)2 heterotetramer
5ZBX 2.58 Å, The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D)
3R45 2.6 Å, Structure of a CENP-A-Histone H4 Heterodimer in complex with chaperone HJURP
6E0P 2.6 Å, Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex…
6E0C 2.63 Å, Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain…
3WTP 2.67 Å, Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3
7PII 2.68 Å, Structure of the human CCAN CENP-A alpha-satellite complex

Browse structure collections

About this viewer

MolViewer shows 6C0W directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.