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Open data
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Basic information
Entry | Database: PDB / ID: 7qoo | ||||||
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Title | Structure of the human inner kinetochore CCAN complex | ||||||
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![]() | CELL CYCLE / INNER KINETOCHORE / CCAN / COMPLEX / DNA BINDING PROTEIN | ||||||
Function / homology | ![]() positive regulation of protein localization to kinetochore / Mis6-Sim4 complex / centromere complex assembly / kinetochore organization / spindle attachment to meiosis I kinetochore / metaphase chromosome alignment / kinetochore binding / centromeric DNA binding / sex differentiation / CENP-A containing chromatin assembly ...positive regulation of protein localization to kinetochore / Mis6-Sim4 complex / centromere complex assembly / kinetochore organization / spindle attachment to meiosis I kinetochore / metaphase chromosome alignment / kinetochore binding / centromeric DNA binding / sex differentiation / CENP-A containing chromatin assembly / chordate embryonic development / negative regulation of epithelial cell apoptotic process / kinetochore assembly / inner kinetochore / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / mitotic sister chromatid segregation / chromosome, centromeric region / centriolar satellite / chromosome organization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / NRIF signals cell death from the nucleus / mitotic spindle organization / chromosome segregation / positive regulation of epithelial cell proliferation / RHO GTPases Activate Formins / kinetochore / nuclear matrix / Separation of Sister Chromatids / actin cytoskeleton / chromosome / mitotic cell cycle / midbody / nuclear body / cell adhesion / protein heterodimerization activity / cell division / apoptotic process / regulation of DNA-templated transcription / nucleolus / signal transduction / DNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||
![]() | Vetter, I.R. / Pesenti, M. / Raisch, T. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structure of the human inner kinetochore CCAN complex and its significance for human centromere organization. Authors: Marion E Pesenti / Tobias Raisch / Duccio Conti / Kai Walstein / Ingrid Hoffmann / Dorothee Vogt / Daniel Prumbaum / Ingrid R Vetter / Stefan Raunser / Andrea Musacchio / ![]() Abstract: Centromeres are specialized chromosome loci that seed the kinetochore, a large protein complex that effects chromosome segregation. A 16-subunit complex, the constitutive centromere associated ...Centromeres are specialized chromosome loci that seed the kinetochore, a large protein complex that effects chromosome segregation. A 16-subunit complex, the constitutive centromere associated network (CCAN), connects between the specialized centromeric chromatin, marked by the histone H3 variant CENP-A, and the spindle-binding moiety of the kinetochore. Here, we report a cryo-electron microscopy structure of human CCAN. We highlight unique features such as the pseudo GTPase CENP-M and report how a crucial CENP-C motif binds the CENP-LN complex. The CCAN structure has implications for the mechanism of specific recognition of the CENP-A nucleosome. A model consistent with our structure depicts the CENP-C-bound nucleosome as connected to the CCAN through extended, flexible regions of CENP-C. An alternative model identifies both CENP-C and CENP-N as specificity determinants but requires CENP-N to bind CENP-A in a mode distinct from the classical nucleosome octamer. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 568 KB | Display | ![]() |
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PDB format | ![]() | 453.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 969.3 KB | Display | ![]() |
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Full document | ![]() | 980.4 KB | Display | |
Data in XML | ![]() | 72.4 KB | Display | |
Data in CIF | ![]() | 106.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 14098MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Centromere protein ... , 14 types, 14 molecules CHIKLMNOPUQRTW
#1: Protein | Mass: 61856.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 28520.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 86820.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein | Mass: 31696.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Protein | Mass: 39039.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#6: Protein | Mass: 19761.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#7: Protein | Mass: 39609.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#8: Protein | Mass: 33830.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#9: Protein | Mass: 33210.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#10: Protein | Mass: 47609.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#11: Protein | Mass: 30648.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#12: Protein | Mass: 20228.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#13: Protein | Mass: 60502.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#14: Protein | Mass: 10087.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules X
#15: Protein/peptide | Mass: 1294.587 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: human inner kinetochore CCAN complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.451 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 6.8 / Details: 0.0025% Triton |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 286 K / Details: blot for 3.5 seconds at blot force -3 |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 76.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 1540 Details: Images were collected in movie mode with 80 frames per image in superresolution mode with 0.35 A/px (0.7A native) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 140910 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25206 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |