6E0P: Centromeric nucleosome

Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex with a single chain antibody fragment. Determined by electron microscopy at 2.6 Å resolution. Released 22 May 2019.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Homo sapiens, Mus musculus
Chains: 12
Atoms: 15,567
Mol. weight: 262.62 kDa
Released: 22 May 2019

Explore 6E0P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E0P contains 46 α-helices and 74 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.

Chains A and E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	47-54	8
α-helix	64-76	13
β-strand	85-86	2	1
α-helix	88-115	28
β-strand	120-121	2	2
α-helix	122	1
α-helix	123-133	11

Chains B and F: 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: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
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	80-88	9
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	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	105-123	19

Chain G: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	17-21	5
α-helix	27-36	10
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
α-helix	113-115	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

Chain M: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	25-28	4	11
β-strand	32-34	3	12
β-strand	40-43	4	13
β-strand	44-47	4	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	129-132	4	12
β-strand	133	1	11
β-strand	136-140	5	12
β-strand	163-164	2	14
β-strand	168-171	4	15
β-strand	177-180	4	16
β-strand	181-182	2	14
β-strand	187	1	17
β-strand	191-196	6	15
β-strand	203-207	5	15
β-strand	211-212	2	15
α-helix	213	1
β-strand	220-225	6	16
β-strand	226	1	17
β-strand	228-233	6	16
β-strand	242-248	7	15
β-strand	255-256	2	15
β-strand	260-264	5	15

Chain N: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	25-28	4	18
β-strand	32-34	3	19
β-strand	39-40	2	20
β-strand	43	1	20
β-strand	44-47	4	18
α-helix	51-53	3
β-strand	54-62	9	19
β-strand	66-74	9	19
β-strand	79-82	4	19
α-helix	84-86	3
β-strand	87	1	20
β-strand	90-95	6	20
β-strand	100-106	7	20
α-helix	110-112	3
β-strand	114-122	9	19
β-strand	129-132	4	19
β-strand	136-140	5	19
β-strand	162-163	2	21
β-strand	168-171	4	19
β-strand	177-180	4	22
β-strand	182-183	2	21
β-strand	191-196	6	19
β-strand	203-207	5	19
β-strand	211-212	2	19
α-helix	213	1
β-strand	220-225	6	22
β-strand	228-233	6	22
β-strand	243-248	6	19
β-strand	255-256	2	19
β-strand	261-264	4	19

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 (145-mer)	I	DNA	145	Homo sapiens
DNA (145-mer)	J	DNA	145	Homo sapiens
scFv	M, N	protein	265	Mus musculus

Sequence of entity 1 (A, E), FASTA

>6E0P_1 Histone H3-like centromeric protein A (chains A, E)
MGSSHHHHHHSSGLPRSHMGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSR
RRQGWLKEIRKLQKSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFL
VHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLEEGLG

Sequence of entity 2 (B, F), FASTA

>6E0P_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6E0P_3 Histone H2A type 1-B/E (chains C, G)
MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>6E0P_4 Histone H2B type 1-J (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 5 (I), FASTA

>6E0P_5 DNA (145-MER) (chains I)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTCTGTGAGTGAAACTCCATCATCACAAAGAATATTCTGAGAATGCTTCCGT
TTGCCTTTTATATGAACTTCCTGAT

Sequence of entity 6 (J), FASTA

>6E0P_6 DNA (145-MER) (chains J)
ATCAGGAAGTTCATATAAAAGGCAAACGGAAGCATTCTCAGAATATTCTTTGTGATGATG
GAGTTTCACTCACAGAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTG
GTAGAATCTGCAGGTGGATATTGAT

Sequence of entity 7 (M, N), FASTA

>6E0P_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
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
7U46 2.68 Å, Cryo-EM structure of CENP-A nucleosome (palindromic alpha satellite DNA) in complex with…

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