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- PDB-28op: Structure of the human inner kinetochore CCAN and CENP-C bound to DNA -

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Entry
Database: PDB / ID: 28op
TitleStructure of the human inner kinetochore CCAN and CENP-C bound to DNA
Components
  • (Centromere protein ...) x 15
  • DNA (59-MER)
  • DNA (61-MER)
  • Methylated-DNA--protein-cysteine methyltransferase,Centromere protein T
KeywordsCELL CYCLE / Centromeres / Kinetochores
Function / homology
Function and homology information


MGMT-mediated DNA damage reversal / FANCM-MHF complex / Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / kinetochore organization / spindle attachment to meiosis I kinetochore / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / Fanconi anaemia nuclear complex / metaphase chromosome alignment ...MGMT-mediated DNA damage reversal / FANCM-MHF complex / Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / kinetochore organization / spindle attachment to meiosis I kinetochore / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / Fanconi anaemia nuclear complex / metaphase chromosome alignment / kinetochore binding / sex differentiation / centromeric DNA binding / chordate embryonic development / DNA-methyltransferase activity / resolution of meiotic recombination intermediates / CENP-A containing chromatin assembly / negative regulation of epithelial cell apoptotic process / kinetochore assembly / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / inner kinetochore / DNA alkylation repair / positive regulation of double-strand break repair / mitotic sister chromatid segregation / replication fork processing / chromosome, centromeric region / chromosome organization / pericentric heterochromatin / interstrand cross-link repair / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / NRIF signals cell death from the nucleus / Resolution of Sister Chromatid Cohesion / positive regulation of epithelial cell proliferation / positive regulation of protein ubiquitination / mitotic spindle organization / methyltransferase activity / Fanconi Anemia Pathway / chromosome segregation / RHO GTPases Activate Formins / PKR-mediated signaling / kinetochore / centriolar satellite / nuclear matrix / Separation of Sister Chromatids / mitotic cell cycle / chromosome / actin cytoskeleton / midbody / methylation / cell adhesion / nuclear body / protein heterodimerization activity / cell division / DNA repair / apoptotic process / DNA damage response / chromatin binding / regulation of DNA-templated transcription / negative regulation of apoptotic process / chromatin / nucleolus / signal transduction / DNA binding / nucleoplasm / membrane / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
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 / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Centromere protein X / Methylated-DNA--protein-cysteine methyltransferase / Centromere protein C / Centromere protein R / Centromere protein W / Centromere protein P / Centromere protein U ...DNA / DNA (> 10) / DNA (> 100) / Centromere protein X / Methylated-DNA--protein-cysteine methyltransferase / Centromere protein C / Centromere protein R / Centromere protein W / Centromere protein P / Centromere protein U / Centromere protein Q / Centromere protein L / Centromere protein S / Centromere protein I / 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)
Trichoplusia ni (cabbage looper)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 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
DepositionFeb 11, 2026Deposition 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: 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
M: Centromere protein M
S: Centromere protein S
T: Methylated-DNA--protein-cysteine methyltransferase,Centromere protein T
U: Centromere protein U
V: DNA (59-MER)
W: Centromere protein W
X: Centromere protein X
Y: DNA (61-MER)
H: Centromere protein H
I: Centromere protein I
K: Centromere protein K
L: Centromere protein L
N: Centromere protein N
O: Centromere protein O
P: Centromere protein P
Q: Centromere protein Q
R: Centromere protein R
C: Centromere protein C,Methylated-DNA--protein-cysteine methyltransferase


Theoretical massNumber of molelcules
Total (without water)720,30418
Polymers720,30418
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, 15 molecules MSUWXHIKLNOPQRC

#1: 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
#2: 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
#4: 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
#6: 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
#7: 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
#9: 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
#10: Protein Centromere protein I / CENP-I / FSH primary response protein 1 / Follicle-stimulating hormone primary response protein / ...CENP-I / FSH primary response protein 1 / Follicle-stimulating hormone primary response protein / Interphase centromere complex protein 19 / Leucine-rich primary response protein 1


Mass: 87615.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPI, FSHPRH1, ICEN19, LRPR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92674
#11: 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
#12: 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
#13: Protein Centromere protein N / CENP-N / Interphase centromere complex protein 32


Mass: 40541.574 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
#14: Protein Centromere protein O / CENP-O / Interphase centromere complex protein 36


Mass: 33830.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPO, ICEN36, MCM21R / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BU64
#15: 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
#16: 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.) Trichoplusia ni (cabbage looper) / Gene: CENPQ, C6orf139 / Production host: Homo sapiens (human) / References: UniProt: Q7L2Z9
#17: 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
#18: Protein Centromere protein C,Methylated-DNA--protein-cysteine methyltransferase / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase


Mass: 86473.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPC, MGMT / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q03188, UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase

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Protein , 1 types, 1 molecules T

#3: Protein Methylated-DNA--protein-cysteine methyltransferase,Centromere protein T / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase / CENP-T / ...6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase / 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: MGMT, CENPT, C16orf56, ICEN22 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P16455, UniProt: Q96BT3, methylated-DNA-[protein]-cysteine S-methyltransferase

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DNA chain , 2 types, 2 molecules VY

#5: DNA chain DNA (59-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)
#8: DNA chain DNA (61-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 modificationY

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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: Structure of the human inner kinetochore CCAN and CENP-C bound to DNA
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
13cryoSPARC4.63D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1260362 / Symmetry type: POINT
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00628731
ELECTRON MICROSCOPYf_angle_d0.91839257
ELECTRON MICROSCOPYf_dihedral_angle_d18.6844734
ELECTRON MICROSCOPYf_chiral_restr0.0494495
ELECTRON MICROSCOPYf_plane_restr0.0164523

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