3AN2: Centromeric nucleosome containing CENP-A

The structure of the centromeric nucleosome containing CENP-A. Determined by X-ray diffraction at 3.6 Å resolution. Released 20 Jul 2011.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 10
Atoms: 10,542
Mol. weight: 204.31 kDa
Released: 20 Jul 2011

Explore 3AN2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3AN2 contains 38 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: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-77	14
β-strand	85-86	2	1
α-helix	88-113	26
β-strand	120-121	2	2
α-helix	129-131	3

Chain B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	32-40	9
β-strand	45-46	2	2
α-helix	49-51	3
α-helix	52-71	20
β-strand	80-81	2	1
α-helix	83-93	11
β-strand	96-97	2	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-35	9
β-strand	43	1	4
α-helix	47-66	20
α-helix	68-72	5
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	102	1	6

Chain D: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	37-39	3
α-helix	41-45	5
β-strand	53-54	2	5
α-helix	58-83	26
β-strand	89	1	4
α-helix	93-99	7
α-helix	104-106	3
α-helix	107-110	4
α-helix	115-122	8

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	51-54	4
α-helix	65-75	11
β-strand	85-86	2	7
α-helix	90-110	21
β-strand	120	1	8
α-helix	129-132	4

Chain F: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45	1	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-93	11
β-strand	98	1	6

Chain G: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	47-72	26
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-101	2	3

Chain H: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-47	10
β-strand	53-54	2	10
α-helix	57-78	22
α-helix	80-83	4
β-strand	88-89	2	9
α-helix	91-101	11
α-helix	104-112	9
α-helix	119-122	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3-like centromeric protein A	A, E	protein	143	Homo sapiens	P49450 (AlphaFold model)
Histone H4	B, F	protein	106	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	133	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-J	D, H	protein	129	Homo sapiens	P06899 (AlphaFold model)
147 mer DNA	I, J	DNA	147

Sequence of entity 1 (A, E), FASTA

>3AN2_1 Histone H3-like centromeric protein A (chains A, E)
GSHMGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSRRRQGWLKEIRKLQKS
THLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAG
RVTLFPKDVQLARRIRGLEEGLG

Sequence of entity 2 (B, F), FASTA

>3AN2_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>3AN2_3 Histone H2A type 1-B/E (chains C, G)
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>3AN2_4 Histone H2B type 1-J (chains D, H)
GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTK
AVTKYTSAK

Sequence of entity 5 (I, J), FASTA

>3AN2_5 147 mer DNA (chains I, J)
ATCCTTCGTTGGAAACGGGATTTCTTCATTTCATGCTAGACAGAAGAATTCTCAGTAACT
TCTTTGTGCTGGTAACCAGCACAAAGAAGTTACTGAGAATTCTTCTGTCTAGCATGAAAT
GAAGAAATCCCGTTTCCAACGAAGGAT

Primary citation

Crystal structure of the human centromeric nucleosome containing CENP-A. Tachiwana, H., Kagawa, W., Shiga, T. et al. Nature (2011) 476:232-235. DOI 10.1038/nature10258 · 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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