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- PDB-9tax: Structure of the human inner kinetochore CCAN bound to a mono-CEN... -

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Database: PDB / ID: 9tax
TitleStructure of the human inner kinetochore CCAN bound to a mono-CENP-A nucleosome
Components
  • (Centromere protein ...) x 15
  • (DNA (199-MER)) x 2
  • Histone H2A type 1-C
  • Histone H2B type 1-C/E/F/G/I
  • Histone H3-like centromeric protein A
  • Histone H4
  • Isoform 3 of Centromere protein N
KeywordsCELL CYCLE / Centromeres / Kinetochores
Function / homology
Function and homology information


FANCM-MHF complex / Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / kinetochore organization / spindle attachment to meiosis I kinetochore / Fanconi anaemia nuclear complex / metaphase chromosome alignment / kinetochore binding / centromeric DNA binding / chordate embryonic development ...FANCM-MHF complex / Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / kinetochore organization / spindle attachment to meiosis I kinetochore / Fanconi anaemia nuclear complex / metaphase chromosome alignment / kinetochore binding / centromeric DNA binding / chordate embryonic development / resolution of meiotic recombination intermediates / CENP-A containing chromatin assembly / negative regulation of epithelial cell apoptotic process / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / inner kinetochore / establishment of mitotic spindle orientation / mitotic cytokinesis / mitotic sister chromatid segregation / replication fork processing / chromosome, centromeric region / chromosome organization / pericentric heterochromatin / interstrand cross-link repair / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / telomere organization / EML4 and NUDC in mitotic spindle formation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / NRIF signals cell death from the nucleus / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Resolution of Sister Chromatid Cohesion / positive regulation of epithelial cell proliferation / positive regulation of protein ubiquitination / DNA methylation / Condensation of Prophase Chromosomes / mitotic spindle organization / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / innate immune response in mucosa / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Fanconi Anemia Pathway / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / chromosome segregation / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKR-mediated signaling / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / kinetochore / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / centriolar satellite / Metalloprotease DUBs / RMTs methylate histone arginines / nuclear matrix / HCMV Early Events / structural constituent of chromatin / Separation of Sister Chromatids / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / mitotic cell cycle / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response
Similarity search - Function
Centromere protein W / : / CENP-W protein / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Centromere subunit L / Centromere protein L / Centromere protein R / Centromere protein Q ...Centromere protein W / : / CENP-W protein / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Centromere subunit L / Centromere protein L / Centromere protein R / Centromere protein Q / Centromere protein P / Kinetochore component, CENP-R / CENP-Q, a CENPA-CAD centromere complex subunit / CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P / Centromere protein H, C-terminal / Centromere protein Cenp-M / Centromere protein Cenp-K / Centromere protein H / Centromere protein H (CENP-H) / Centromere protein M (CENP-M) / Centromere-associated protein K / Centromere protein I / Mis6 / Centromere protein U / CENP-A nucleosome associated complex (NAC) subunit / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / Kinetochore assembly subunit CENP-C, N-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Centromere protein O / : / Cenp-O kinetochore centromere component / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Centromere protein I / Centromere protein X / Histone H3-like centromeric protein A / Histone H4 / Histone H2B type 1-C/E/F/G/I / Centromere protein C / Centromere protein R ...DNA / DNA (> 10) / DNA (> 100) / Centromere protein I / Centromere protein X / Histone H3-like centromeric protein A / Histone H4 / Histone H2B type 1-C/E/F/G/I / Centromere protein C / Centromere protein R / Centromere protein W / Centromere protein P / Centromere protein U / Centromere protein Q / Centromere protein L / Centromere protein S / Histone H2A type 1-C / Centromere protein T / Centromere protein N / Centromere protein K / Centromere protein O / Centromere protein H / Centromere protein M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsYu, C. / Barford, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_120 United Kingdom
Cancer Research UKC576/A25675 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Models for the architecture of the human inner kinetochore on centromeric α-satellite CENP-A nucleosome arrays.
Authors: Cong Yu / Kyle W Muir / Jing Yang / Ziguo Zhang / Stephen H McLaughlin / David Barford /
Abstract: Human kinetochores assemble onto centromeric DNA comprising repetitive arrays of the 171 bp α-satellite sequence. To understand the higher-order architecture of the inner kinetochore assembled ...Human kinetochores assemble onto centromeric DNA comprising repetitive arrays of the 171 bp α-satellite sequence. To understand the higher-order architecture of the inner kinetochore assembled onto α-satellite arrays, we show cryo-EM structures of CCAN with free DNA, and α-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 α-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 α-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 α-satellite chromatin containing CENP-A nucleosomes.
History
DepositionNov 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Centromere protein H
I: Centromere protein I
K: Centromere protein K
M: Centromere protein M
L: Centromere protein L
N: Isoform 3 of Centromere protein N
O: Centromere protein O
P: Centromere protein P
Q: Centromere protein Q
U: Centromere protein U
R: Centromere protein R
T: Centromere protein T
W: Centromere protein W
S: Centromere protein S
X: Centromere protein X
V: DNA (199-MER)
Y: DNA (199-MER)
a: Centromere protein C
b: Centromere protein C
c: Histone H3-like centromeric protein A
d: Histone H4
e: Histone H2A type 1-C
f: Histone H2B type 1-C/E/F/G/I
g: Histone H3-like centromeric protein A
h: Histone H4
i: Histone H2A type 1-C
j: Histone H2B type 1-C/E/F/G/I


Theoretical massNumber of molelcules
Total (without water)922,82027
Polymers922,82027
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Centromere protein ... , 15 types, 16 molecules HIKMLOPQURTWSXab

#1: Protein Centromere protein H


Mass: 28520.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPH / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H3R5
#2: Protein Centromere protein I


Mass: 87615.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPI / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8C8KX99
#3: Protein Centromere protein K


Mass: 31696.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPK / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BS16
#4: Protein Centromere protein M


Mass: 19761.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPM / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NSP4
#5: Protein Centromere protein L / CENP-L / Interphase centromere complex protein 33


Mass: 39364.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPL, C1orf155, ICEN33 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N0S6
#7: Protein Centromere protein O


Mass: 33830.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPO / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BU64
#8: Protein Centromere protein P


Mass: 33210.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6IPU0
#9: Protein Centromere protein Q / CENP-Q


Mass: 24634.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPQ, C6orf139 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7L2Z9
#10: Protein Centromere protein U / CENP-U / Centromere protein of 50 kDa / CENP-50 / Interphase centromere complex protein 24 / KSHV ...CENP-U / Centromere protein of 50 kDa / CENP-50 / Interphase centromere complex protein 24 / KSHV latent nuclear antigen-interacting protein 1 / MLF1-interacting protein / Polo-box-interacting protein 1


Mass: 24484.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPU, ICEN24, KLIP1, MLF1IP, PBIP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q71F23
#11: Protein Centromere protein R


Mass: 20228.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3BP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13352
#12: Protein Centromere protein T / CENP-T / Interphase centromere complex protein 22


Mass: 84067.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPT, C16orf56, ICEN22 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96BT3
#13: Protein Centromere protein W


Mass: 10087.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPW / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5EE01
#14: Protein Centromere protein S


Mass: 15917.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N2Z9
#15: Protein Centromere protein X


Mass: 8972.415 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPX / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8MT69
#18: Protein Centromere protein C


Mass: 86473.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03188

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Protein , 5 types, 9 molecules Ncgdheifj

#6: Protein Isoform 3 of Centromere protein N / CENP-N / Interphase centromere complex protein 32


Mass: 40541.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPN, C16orf60, ICEN32, BM-309 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96H22
#19: Protein Histone H3-like centromeric protein A


Mass: 16023.630 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49450
#20: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62805
#21: Protein Histone H2A type 1-C / H2A-clustered histone 6 / Histone H2A/l


Mass: 16666.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC6, H2AFL, HIST1H2AC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q93077
#22: Protein Histone H2B type 1-C/E/F/G/I / Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone ...Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone H2B.k / H2B/k / Histone H2B.l / H2B/l


Mass: 13937.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62807

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DNA chain , 2 types, 2 molecules VY

#16: DNA chain DNA (199-MER)


Mass: 65387.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#17: DNA chain DNA (199-MER)


Mass: 65508.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human inner kinetochore CCAN bound to a mono-CENP-A nucleosome
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2PHENIX1.21.2_5419model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39306 / Symmetry type: POINT
RefinementHighest resolution: 4.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00441743
ELECTRON MICROSCOPYf_angle_d0.61657993
ELECTRON MICROSCOPYf_dihedral_angle_d24.7138661
ELECTRON MICROSCOPYf_chiral_restr0.0386603
ELECTRON MICROSCOPYf_plane_restr0.0045925

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