9TAY image
Deposition Date 2025-11-18
Release Date 2026-05-20
Last Version Date 2026-07-29
Entry Detail
PDB ID:
9TAY
Keywords:
CELL CYCLE
Title:
Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Mus musculus (Taxon ID: 10090)
Expression System(s):
Trichoplusia ni, Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
15.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9TAY validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3-like centromeric p
Gene (Uniprot):CENPA
Chain IDs:P (auth: A), T (auth: E), BA (auth: c), FA (auth: g)
Chain Length:0
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:P49450 Pfam ID:PF00125
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16
Chain IDs:Q (auth: B), U (auth: F), CA (auth: d), GA (auth: h)
Chain Length:0
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:P62805 Pfam ID:PF15511
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-C
Gene (Uniprot):H2AC6
Chain IDs:R (auth: C), V (auth: G), DA (auth: e), HA (auth: i)
Chain Length:0
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:Q93077 Pfam ID:PF00125, PF16211
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-C/E/F/G/I
Gene (Uniprot):H2BC4, H2BC6, H2BC7, H2BC8, H2BC10
Chain IDs:S (auth: D), W (auth: J), EA (auth: f), IA (auth: j)
Chain Length:0
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:P62807 Pfam ID:PF00125
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein H
Gene (Uniprot):CENPH
Chain IDs:A (auth: H)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H3R5 Pfam ID:PF05837
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein I
Gene (Uniprot):CENPI
Chain IDs:B (auth: I)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q92674 Pfam ID:PF07778
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein K
Gene (Uniprot):CENPK
Chain IDs:C (auth: K)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BS16 Pfam ID:PF11802
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein L
Gene (Uniprot):CENPL
Chain IDs:D (auth: L)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N0S6 Pfam ID:PF13092
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein M
Gene (Uniprot):CENPM
Chain IDs:E (auth: M)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NSP4 Pfam ID:PF11111
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein N
Gene (Uniprot):CENPN
Chain IDs:F (auth: N)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96H22 Pfam ID:PF05238
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein O
Gene (Uniprot):CENPO
Chain IDs:G (auth: O)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BU64 Pfam ID:PF09496
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein P
Gene (Uniprot):CENPP
Chain IDs:J (auth: P)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6IPU0 Pfam ID:PF13096
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein Q
Gene (Uniprot):CENPQ
Chain IDs:H (auth: Q)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7L2Z9 Pfam ID:PF13094
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein R
Gene (Uniprot):ITGB3BP
Chain IDs:K (auth: R)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13352 Pfam ID:PF06729
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein S
Gene (Uniprot):CENPS
Chain IDs:N (auth: S)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N2Z9 Pfam ID:PF15630
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Methylated-DNA--protein-cyste
Gene (Uniprot):MGMT, CENPT
Chain IDs:L (auth: T)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P16455,Q96BT3 Pfam ID:PF02870, PF01035, PF16171, PF15511 EC:2.1.1.63
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein U
Gene (Uniprot):CENPU
Chain IDs:I (auth: U)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q71F23 Pfam ID:PF13097
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (318-MER)
Chain IDs:X (auth: V)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein W
Gene (Uniprot):CENPW
Chain IDs:M (auth: W)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q5EE01 Pfam ID:PF15510
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centromere protein X
Gene (Uniprot):CENPX
Chain IDs:O (auth: X)
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:A8MT69 Pfam ID:PF09415
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (318-MER)
Chain IDs:Y
Chain Length:0
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:scFv
Chain IDs:Z, AA (auth: a), JA (auth: m), KA (auth: n)
Chain Length:0
Number of Molecules:4
Biological Source:Mus musculus
Ligand Molecules
NA
Primary Citation
Models for the architecture of the human inner kinetochore on centromeric alpha-satellite CENP-A nucleosome arrays.
Nat Commun 17 ? ? (2026)
PMID: 42120391 DOI: 10.1038/s41467-026-72856-0

Abstact

Human kinetochores assemble onto centromeric DNA comprising repetitive arrays of the 171 bp alpha-satellite sequence. To understand the higher-order architecture of the inner kinetochore assembled onto alpha-satellite arrays, we show cryo-EM structures of CCAN with free DNA, and alpha-satellite repeat monomers and dimers with CENP-A nucleosomes. CCAN bound to free DNA and a monomeric CENP-A nucleosome engages 70 bp of DNA comprising 30 bp of an upstream alpha-satellite repeat. This upstream DNA interacts with the histone-fold domain subunits of the CENP-TWSX module in a manner resembling how nucleosomes wrap DNA gyres. A complex of CCAN assembled onto a dimeric alpha-satellite repeat with two CENP-A nucleosomes shows that CCAN can only be accommodated on the linker DNA by unwrapping DNA from both the CENP-TWSX module and the upstream nucleosome. We discuss the implications of these results for models of CCAN assembly on arrays of alpha-satellite chromatin containing CENP-A nucleosomes.

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Primary Citation of related structures
9TAY
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