7U46: CENP-A nucleosome
Cryo-EM structure of CENP-A nucleosome (palindromic alpha satellite DNA) in complex with CENP-N. Determined by electron microscopy at 2.68 Å resolution. Released 16 Mar 2022.
- Method
- Electron microscopy
- Resolution
- 2.68 Å
- Organisms
- Homo sapiens, Escherichia coli
- Chains
- 11
- Atoms
- 13,360
- Mol. weight
- 236.58 kDa
- Released
- 16 Mar 2022
Explore 7U46 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7U46 contains 42 α-helices and 26 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 | 47-56 | 10 | |
| 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: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-97 | 2 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| 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 | 93-96 | 4 | |
| β-strand | 101-102 | 2 | 6 |
Chains D and H: 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 | 105-122 | 18 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-55 | 9 | |
| α-helix | 64-77 | 14 | |
| β-strand | 85-86 | 2 | 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 | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 6 |
Chain G: 5 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 | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-101 | 2 | 3 |
Chain K: 10 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-14 | 12 | |
| α-helix | 21-28 | 8 | |
| α-helix | 33-38 | 6 | |
| α-helix | 45-58 | 14 | |
| α-helix | 63-76 | 14 | |
| α-helix | 78-80 | 3 | |
| β-strand | 83-89 | 7 | 11 |
| α-helix | 101-115 | 15 | |
| β-strand | 120-126 | 7 | 11 |
| β-strand | 130-136 | 7 | 11 |
| α-helix | 143-145 | 3 | |
| β-strand | 150-155 | 6 | 11 |
| β-strand | 160-164 | 5 | 11 |
| α-helix | 172-182 | 11 | |
| β-strand | 187-195 | 9 | 11 |
| α-helix | 198-210 | 13 | |
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 | C, G | protein | 130 | Homo sapiens | Q93077 (AlphaFold model) |
| Histone H2B type 1-C/E/F/G/I | D, H | protein | 126 | Homo sapiens | P62807 (AlphaFold model) |
| Centromere protein N | K | protein | 295 | Homo sapiens | Q96H22 |
| DNA (147-mer) | I | DNA | 147 | Escherichia coli | |
| DNA (147-mer) | J | DNA | 147 | Escherichia coli | |
Sequence of entity 1 (A, E), FASTA
>7U46_1 Histone H3-like centromeric protein A (chains A, E)
MGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSRRRQGWLKEIRKLQKSTHL
LIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVT
LFPKDVQLARRIRGLEEGLG
Sequence of entity 2 (B, F), FASTA
>7U46_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>7U46_3 Histone H2A (chains C, G)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>7U46_4 Histone H2B type 1-C/E/F/G/I (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK
Sequence of entity 5 (K), FASTA
>7U46_5 Centromere protein N (chains K)
MDETVAEFIKRTILKIPMNELTTILKAWDFLSENQLQTVNFRQRKESVVQHLIHLCEEKR
ASISDAALLDIIYMQFHQHQKVWDVFQMSKGPGEDVDLFDMKQFKNSFKKILQRALKNVT
VSFRETEENAVWIRIAWGTQYTKPNQYKPTYVVYYSQTPYAFTSSSMLRRNTPLLGQALT
IASKHHQIVKMDLRSRYLDSLKAIVFKQYNQTFETHNSTTPLQERSLGLDINMDSRIIHE
NIVEKERVQRITQETFGDYPQPQLEFAQYKLETKFKSGLNGSILAEREEHHHHHH
Sequence of entity 6 (I), FASTA
>7U46_6 DNA (147-MER) (chains I)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTT
TGGTAGTATCTGCAGGTGGATATTGAT
Sequence of entity 7 (J), FASTA
>7U46_7 DNA (147-MER) (chains J)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTT
TGGTAGTATCTGCAGGTGGATATTGAT
Primary citation
CENP-N promotes the compaction of centromeric chromatin. Zhou, K., Gebala, M., Woods, D. et al. Nat Struct Mol Biol (2022) 29:403-413. DOI 10.1038/s41594-022-00758-y · 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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