6E0C: CENP-A nucleosome

Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain antibody fragment. Determined by electron microscopy at 2.63 Å resolution. Released 22 May 2019.

Method: Electron microscopy
Resolution: 2.63 Å
Organisms: Homo sapiens, Escherichia coli, Mus musculus
Chains: 12
Atoms: 15,608
Mol. weight: 263.88 kDa
Released: 22 May 2019

Explore 6E0C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E0C contains 44 α-helices and 76 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	47-54	8
α-helix	64-76	13
α-helix	82-84	3
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	83-91	9
β-strand	96-98	3	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	17-21	5
α-helix	27-35	9
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

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	105-123	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	47-54	8
α-helix	64-75	12
α-helix	82-84	3
β-strand	85-86	2	7
α-helix	88-115	28
β-strand	120-121	2	8
α-helix	123-133	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	80-81	2	7
α-helix	83-91	9
β-strand	96-98	3	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	17-21	5
α-helix	27-35	9
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

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	105-122	18

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
Histone H3-like centromeric protein A	A, E	protein	158	Homo sapiens	P49450 (AlphaFold model)
Histone H4	B, F	protein	103	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	130	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-J	D, H	protein	126	Homo sapiens	P06899 (AlphaFold model)
DNA (146-mer)	I	DNA	147	Escherichia coli
DNA (146-mer)	J	DNA	147	Escherichia coli
scFv	M, N	protein	265	Mus musculus

Sequence of entity 1 (A, E), FASTA

>6E0C_1 Histone H3-like centromeric protein A (chains A, E)
MGSSHHHHHHSSGLPRSHMGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSR
RRQGWLKEIRKLQKSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFL
VHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLEEGLG

Sequence of entity 2 (B, F), FASTA

>6E0C_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6E0C_3 Histone H2A type 1-B/E (chains C, G)
MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>6E0C_4 Histone H2B type 1-J (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 5 (I), FASTA

>6E0C_5 DNA (146-MER) (chains I)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT

Sequence of entity 6 (J), FASTA

>6E0C_6 DNA (146-MER) (chains J)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT

Sequence of entity 7 (M, N), FASTA

>6E0C_7 scFv (chains M, N)
MKSSHHHHHHENLYFQSNAMEVQLQQSGPELVEPGTSVKMPCKASGYTFTSYTIQWVKQT
PRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSEDSAVYYCARKS
SRLRSTLDYWGQGTSVTVSSGGGGSGGGGSGGGGSMDIKMTQSPSSMHASLGERVTITCK
ASQDIRSYLSWYQQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTA
TYYCLQHGESPYTFGSGTKLEIKRA

Primary citation

Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment. Zhou, B.R., Yadav, K.N.S., Borgnia, M. et al. Nat Commun (2019) 10:2301-2301. DOI 10.1038/s41467-019-10247-4 · 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…
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
7U46 2.68 Å, Cryo-EM structure of CENP-A nucleosome (palindromic alpha satellite DNA) in complex with…

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