+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14098 | |||||||||
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Title | Structure of the human inner kinetochore CCAN complex | |||||||||
Map data | main map | |||||||||
Sample |
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Keywords | INNER KINETOCHORE / CCAN / COMPLEX / DNA BINDING PROTEIN / CELL CYCLE | |||||||||
Function / homology | Function and homology information 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 / sex differentiation / centromeric DNA binding / 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 / sex differentiation / centromeric DNA binding / 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 / positive regulation of epithelial cell proliferation / chromosome segregation / 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 / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Vetter IR / Pesenti M / Raisch T | |||||||||
Funding support | 1 items
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Citation | Journal: Mol Cell / Year: 2022 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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14098.map.gz | 201 MB | EMDB map data format | |
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Header (meta data) | emd-14098-v30.xml emd-14098.xml | 31.2 KB 31.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14098_fsc.xml emd_14098_fsc_2.xml | 13.8 KB 13.8 KB | Display Display | FSC data file |
Images | emd_14098.png | 195.5 KB | ||
Masks | emd_14098_msk_1.map emd_14098_msk_2.map emd_14098_msk_3.map | 216 MB 216 MB 216 MB | Mask map | |
Filedesc metadata | emd-14098.cif.gz | 9.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14098 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14098 | HTTPS FTP |
-Validation report
Summary document | emd_14098_validation.pdf.gz | 672.1 KB | Display | EMDB validaton report |
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Full document | emd_14098_full_validation.pdf.gz | 671.7 KB | Display | |
Data in XML | emd_14098_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | emd_14098_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14098 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14098 | HTTPS FTP |
-Related structure data
Related structure data | 7qooMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14098.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.7 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14098_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_14098_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #3
File | emd_14098_msk_3.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human inner kinetochore CCAN complex
+Supramolecule #1: human inner kinetochore CCAN complex
+Macromolecule #1: Centromere protein C
+Macromolecule #2: Centromere protein H
+Macromolecule #3: Centromere protein I
+Macromolecule #4: Centromere protein K
+Macromolecule #5: Centromere protein L
+Macromolecule #6: Centromere protein M
+Macromolecule #7: Centromere protein N
+Macromolecule #8: Centromere protein O
+Macromolecule #9: Centromere protein P
+Macromolecule #10: Centromere protein U
+Macromolecule #11: Centromere protein Q
+Macromolecule #12: Centromere protein R
+Macromolecule #13: Centromere protein T
+Macromolecule #14: Centromere protein W
+Macromolecule #15: Unknown protein
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 6.8 / Details: 0.0025% Triton |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3.5 seconds at blot force -3. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 1540 / Average electron dose: 76.8 e/Å2 Details: Images were collected in movie mode with 80 frames per image in superresolution mode with 0.35 A/px (0.7A native) |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7qoo: |