6SE6: Class2 : CENP-A nucleosome

Class2 : CENP-A nucleosome in complex with CENP-C central region. Determined by electron microscopy at 3.5 Å resolution. Released 14 Aug 2019.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Homo sapiens, synthetic construct
Chains: 11
Atoms: 12,068
Mol. weight: 214.68 kDa
Released: 14 Aug 2019

Explore 6SE6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SE6 contains 35 α-helices and 20 β-strands across 8 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	46-56	11
α-helix	64-75	12
β-strand	85-86	2	1
α-helix	88-115	28
β-strand	120-121	2	2
α-helix	123-133	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-93	11
β-strand	97	1	3

Chain C: 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	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	93-96	4
β-strand	100-102	3	6
α-helix	106-108	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	105-121	17

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	46-56	11
α-helix	64-76	13
β-strand	86	1	7
α-helix	88-115	28
β-strand	120-121	2	8
α-helix	123-133	11

Chain F: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	51-75	25
β-strand	81	1	7
α-helix	83-93	11
β-strand	96-98	3	6

Chain 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	9
α-helix	47-71	25
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-96	6
β-strand	101	1	3
α-helix	106-109	4

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	10
α-helix	56-83	28
β-strand	88-89	2	9
α-helix	91-101	11
α-helix	105-123	19

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	103	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 2-A	C, G	protein	130	Homo sapiens	Q6FI13 (AlphaFold model)
Histone H2B type 1-C/E/F/G/I	D, H	protein	126	Homo sapiens	P62807 (AlphaFold model)
DNA (145-mer)	I	DNA	145	synthetic construct
DNA (145-mer)	J	DNA	145	synthetic construct
Centromere protein C	V	protein	124	Homo sapiens	Q03188

Sequence of entity 1 (A, E), FASTA

>6SE6_1 Histone H3-like centromeric protein A (chains A, E)
MGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSRRRQGWLKEIRKLQKSTHL
LIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVT
LFPKDVQLARRIRGLEEGLG

Sequence of entity 2 (B, F), FASTA

>6SE6_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6SE6_3 Histone H2A type 2-A (chains C, G)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>6SE6_4 Histone H2B type 1-C/E/F/G/I (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK

Sequence of entity 5 (I), FASTA

>6SE6_5 DNA (145-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT

Sequence of entity 6 (J), FASTA

>6SE6_6 DNA (145-MER) (chains J)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT

Sequence of entity 7 (V), FASTA

>6SE6_7 Centromere protein C (chains V)
GPLGSPEFGRATMAKPAEEQLDVGQSKDENIHTSHITQDEFQRNSDRNMEEHEEMGNDCV
SKKQMPPVGSKKSSTRKDKEESKKKRFSSESKNKLVPEEVTSTVTKSRRISRRPSDWWVV
KSEE

Primary citation

CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail. Ali-Ahmad, A., Bilokapic, S., Schafer, I.B. et al. EMBO Rep (2019) 20:e48913-e48913. DOI 10.15252/embr.201948913 · 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

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