6O1D: Histone H3-like centromeric protein A
Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA. Determined by electron microscopy at 3.4 Å resolution. Released 22 May 2019.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 11,982
- Mol. weight
- 204.56 kDa
- Released
- 22 May 2019
Explore 6O1D in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6O1D 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: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-55 | 9 | |
| α-helix | 64-68 | 5 | |
| α-helix | 70-74 | 5 | |
| β-strand | 85-86 | 2 | 1 |
| α-helix | 95-100 | 6 | |
| α-helix | 102-115 | 14 | |
| 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 | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 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 | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 93-96 | 4 | |
| 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 | 57-83 | 27 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-123 | 19 | |
Chain E: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-55 | 9 | |
| α-helix | 64-68 | 5 | |
| α-helix | 70-74 | 5 | |
| α-helix | 76-78 | 3 | |
| β-strand | 85-86 | 2 | 7 |
| α-helix | 90-115 | 26 | |
| β-strand | 120-121 | 2 | 8 |
| α-helix | 123-132 | 10 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| 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: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-14 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 47-72 | 26 | |
| β-strand | 78 | 1 | 10 |
| α-helix | 81-88 | 8 | |
| α-helix | 93-96 | 4 | |
| β-strand | 100-102 | 3 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 54 | 1 | 10 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 9 |
| α-helix | 91-101 | 11 | |
| α-helix | 109-121 | 13 | |
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 | |
Sequence of entity 1 (A, E), FASTA
>6O1D_1 Histone H3-like centromeric protein A (chains A, E)
MGSSHHHHHHSSGLPRSHMGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHSR
RRQGWLKEIRKLQKSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFL
VHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLEEGLG
Sequence of entity 2 (B, F), FASTA
>6O1D_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6O1D_3 Histone H2A type 1-B/E (chains C, G)
MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>6O1D_4 Histone H2B type 1-J (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (I), FASTA
>6O1D_5 DNA (145-MER) (chains I)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTCTGTGAGTGAAACTCCATCATCACAAAGAATATTCTGAGAATGCTTCCGT
TTGCCTTTTATATGAACTTCCTGAT
Sequence of entity 6 (J), FASTA
>6O1D_6 DNA (145-MER) (chains J)
ATCAGGAAGTTCATATAAAAGGCAAACGGAAGCATTCTCAGAATATTCTTTGTGATGATG
GAGTTTCACTCACAGAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTG
GTAGAATCTGCAGGTGGATATTGAT
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…
- 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
About this viewer
MolViewer shows 6O1D directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.