+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17814 | |||||||||
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Title | Structure of the human outer kinetochore KMN network complex | |||||||||
Map data | Masked KMN network junction complex | |||||||||
Sample |
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Keywords | Kinetochore / complex / KMN / CELL CYCLE | |||||||||
Function / homology | Function and homology information regulation of meiosis I spindle assembly checkpoint / Knl1/Spc105 complex / positive regulation of meiosis I spindle assembly checkpoint / homologous chromosome orientation in meiotic metaphase I / MIS12/MIND type complex / skeletal muscle satellite cell proliferation / Ndc80 complex / leucine zipper domain binding / acrosome assembly / regulation of mitotic cell cycle spindle assembly checkpoint ...regulation of meiosis I spindle assembly checkpoint / Knl1/Spc105 complex / positive regulation of meiosis I spindle assembly checkpoint / homologous chromosome orientation in meiotic metaphase I / MIS12/MIND type complex / skeletal muscle satellite cell proliferation / Ndc80 complex / leucine zipper domain binding / acrosome assembly / regulation of mitotic cell cycle spindle assembly checkpoint / attachment of spindle microtubules to kinetochore / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / protein localization to kinetochore / mitotic spindle assembly checkpoint signaling / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / acrosomal vesicle / chromosome segregation / RHO GTPases Activate Formins / establishment of localization in cell / kinetochore / fibrillar center / spindle pole / Separation of Sister Chromatids / azurophil granule lumen / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / nuclear body / nuclear speck / cell division / intracellular membrane-bounded organelle / dendrite / Neutrophil degranulation / nucleolus / Golgi apparatus / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Yatskevich S / Barford D | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structure of the human outer kinetochore KMN network complex. Authors: Stanislau Yatskevich / Jing Yang / Dom Bellini / Ziguo Zhang / David Barford / Abstract: Faithful chromosome segregation requires robust, load-bearing attachments of chromosomes to the mitotic spindle, a function accomplished by large macromolecular complexes termed kinetochores. In most ...Faithful chromosome segregation requires robust, load-bearing attachments of chromosomes to the mitotic spindle, a function accomplished by large macromolecular complexes termed kinetochores. In most eukaryotes, the constitutive centromere-associated network (CCAN) complex of the inner kinetochore recruits to centromeres the ten-subunit outer kinetochore KMN network that comprises the KNL1C, MIS12C and NDC80C complexes. The KMN network directly attaches CCAN to microtubules through MIS12C and NDC80C. Here, we determined a high-resolution cryo-EM structure of the human KMN network. This showed an intricate and extensive assembly of KMN subunits, with the central MIS12C forming rigid interfaces with NDC80C and KNL1C, augmented by multiple peptidic inter-subunit connections. We also observed that unphosphorylated MIS12C exists in an auto-inhibited state that suppresses its capacity to interact with CCAN. Ser100 and Ser109 of the N-terminal segment of the MIS12C subunit Dsn1, two key targets of Aurora B kinase, directly stabilize this auto-inhibition. Our study indicates how selectively relieving this auto-inhibition through Ser100 and Ser109 phosphorylation might restrict outer kinetochore assembly to functional centromeres during cell division. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17814.map.gz | 19.3 MB | EMDB map data format | |
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Header (meta data) | emd-17814-v30.xml emd-17814.xml | 32.8 KB 32.8 KB | Display Display | EMDB header |
Images | emd_17814.png | 19.7 KB | ||
Filedesc metadata | emd-17814.cif.gz | 8.6 KB | ||
Others | emd_17814_additional_1.map.gz emd_17814_additional_2.map.gz emd_17814_additional_3.map.gz emd_17814_additional_4.map.gz emd_17814_half_map_1.map.gz emd_17814_half_map_2.map.gz | 273 MB 16.3 MB 17.4 MB 240.4 MB 273.7 MB 273.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17814 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17814 | HTTPS FTP |
-Related structure data
Related structure data | 8pprMC 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_17814.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Masked KMN network junction complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unmasked KMN network junction complex
File | emd_17814_additional_1.map | ||||||||||||
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Annotation | Unmasked KMN network junction complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: MultiBody refined MIS12C heads
File | emd_17814_additional_2.map | ||||||||||||
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Annotation | MultiBody refined MIS12C heads | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: MultiBody refined KMN junction
File | emd_17814_additional_3.map | ||||||||||||
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Annotation | MultiBody refined KMN junction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: MultiBody refined Spc24/Spc25 coiled-coils
File | emd_17814_additional_4.map | ||||||||||||
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Annotation | MultiBody refined Spc24/Spc25 coiled-coils | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_17814_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2
File | emd_17814_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Outer kinetochore KMN network junction complex
+Supramolecule #1: Outer kinetochore KMN network junction complex
+Macromolecule #1: Kinetochore-associated protein DSN1 homolog
+Macromolecule #2: Protein MIS12 homolog
+Macromolecule #3: Kinetochore-associated protein NSL1 homolog
+Macromolecule #4: Polyamine-modulated factor 1
+Macromolecule #5: Kinetochore protein Spc24
+Macromolecule #6: Kinetochore protein Spc25
+Macromolecule #7: Kinetochore scaffold 1
+Macromolecule #8: ZW10 interactor
+Macromolecule #9: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 599831 |