+Open data
-Basic information
Entry | Database: PDB / ID: 3iz0 | ||||||
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Title | Human Ndc80 Bonsai Decorated Microtubule | ||||||
Components |
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Keywords | CELL CYCLE / Ndc80 / HEC1 / NUF2 / tubulin / kinetochore / mitosis / calponin homology domain / microtubule | ||||||
Function / homology | Function and homology information G2/MI transition of meiotic cell cycle / kinetochore adaptor activity / skeletal muscle satellite cell proliferation / kinetochore => GO:0000776 / Ndc80 complex / kinetochore organization / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / meiotic chromosome segregation / attachment of spindle microtubules to kinetochore ...G2/MI transition of meiotic cell cycle / kinetochore adaptor activity / skeletal muscle satellite cell proliferation / kinetochore => GO:0000776 / Ndc80 complex / kinetochore organization / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / meiotic chromosome segregation / attachment of spindle microtubules to kinetochore / centrosome duplication / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / spindle assembly involved in female meiosis I / positive regulation of axon guidance / cell cycle / mitotic spindle assembly checkpoint signaling / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / microtubule-based process / chromosome, centromeric region / cyclin binding / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / chromosome segregation / RHO GTPases Activate Formins / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / regulation of protein stability / structural constituent of cytoskeleton / kinetochore / microtubule cytoskeleton organization / Separation of Sister Chromatids / microtubule cytoskeleton / mitotic cell cycle / nervous system development / microtubule binding / microtubule / protein heterodimerization activity / cell division / GTPase activity / centrosome / protein-containing complex binding / nucleolus / GTP binding / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 8.6 Å | ||||||
Authors | Alushin, G.M. / Ramey, V.H. / Pasqualato, S. / Ball, D.A. / Grigorieff, N. / Musacchio, A. / Nogales, E. | ||||||
Citation | Journal: Nature / Year: 2010 Title: The Ndc80 kinetochore complex forms oligomeric arrays along microtubules. Authors: Gregory M Alushin / Vincent H Ramey / Sebastiano Pasqualato / David A Ball / Nikolaus Grigorieff / Andrea Musacchio / Eva Nogales / Abstract: The Ndc80 complex is a key site of regulated kinetochore-microtubule attachment (a process required for cell division), but the molecular mechanism underlying its function remains unknown. Here we ...The Ndc80 complex is a key site of regulated kinetochore-microtubule attachment (a process required for cell division), but the molecular mechanism underlying its function remains unknown. Here we present a subnanometre-resolution cryo-electron microscopy reconstruction of the human Ndc80 complex bound to microtubules, sufficient for precise docking of crystal structures of the component proteins. We find that the Ndc80 complex binds the microtubule with a tubulin monomer repeat, recognizing α- and β-tubulin at both intra- and inter-tubulin dimer interfaces in a manner that is sensitive to tubulin conformation. Furthermore, Ndc80 complexes self-associate along protofilaments through interactions mediated by the amino-terminal tail of the NDC80 protein, which is the site of phospho-regulation by Aurora B kinase. The complex's mode of interaction with the microtubule and its oligomerization suggest a mechanism by which Aurora B could regulate the stability of load-bearing kinetochore-microtubule attachments. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3iz0.cif.gz | 324.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iz0.ent.gz | 252.6 KB | Display | PDB format |
PDBx/mmJSON format | 3iz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iz0_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3iz0_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3iz0_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 3iz0_validation.cif.gz | 86.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/3iz0 ftp://data.pdbj.org/pub/pdb/validation_reports/iz/3iz0 | HTTPS FTP |
-Related structure data
Related structure data | 5223MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Details | AUTHORS STATE THAT THE NDC80 COMPLEX FORMS OLIGOMERS ALONG MICROTUBULE PROTOFILAMENTS, BINDING ONCE PER TUBULIN MONOMER. THIS ENTRY CONSISTS OF COORDINATES FOR ONE TUBULIN HETERODIMER BOUND TO A CLUSTER OF 2 NDC80 MOLECULES. THE BINDING SITE IS FORMED BETWEEN TUBULIN MONOMERS, AND THUS THERE IS ONE COMPLETE NDC80-TUBULIN INTERFACE AND ONE NDC80-NDC80 INTERFACE. LARGER CLUSTERS ARE MORE PREVALENT IN VITRO AND ARE LIKELY TO EXIST IN VIVO. |
-Components
-Protein , 4 types, 6 molecules ABCEDF
#1: Protein | Mass: 50107.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cellular location: cytoskeleton / Tissue: brain / References: UniProt: P81947*PLUS | ||
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#2: Protein | Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cellular location: cytoskeleton / Tissue: brain / References: UniProt: Q6B856*PLUS | ||
#3: Protein | Mass: 36351.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NDC80 SPC25, SPBC25, AD024 / Plasmid: pGEX6p-2RBS / Production host: Escherichia coli (E. coli) References: UniProt: Q05DQ6, UniProt: Q9HBM1, UniProt: O14777*PLUS #4: Protein | Mass: 28993.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUF2, RP11-77M5.2-004, SPC24 / Plasmid: pGEX6p-2RBS / Production host: Escherichia coli (E. coli) References: UniProt: B1AQT4, UniProt: C9JGC4, UniProt: Q9BZD4*PLUS |
-Non-polymers , 5 types, 5 molecules
#5: Chemical | ChemComp-ZN / |
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#6: Chemical | ChemComp-MG / |
#7: Chemical | ChemComp-GTP / |
#8: Chemical | ChemComp-GDP / |
#9: Chemical | ChemComp-TA1 / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 0.26 MDa / Experimental value: NO | |||||||||||||||||||||||||
Buffer solution | pH: 6.8 Details: 80mM PIPES, 1mM MgCl2, 1mM EGTA, 1mM DTT, 0.05% Nonidet P-40, 20uM taxol | |||||||||||||||||||||||||
Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: 80mM PIPES, 1mM MgCl2, 1mM EGTA, 1mM DTT, 0.05% Nonidet P-40, 20uM taxol | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % Method: 2ul of 0.25 mg per ml MTs applied to grid for 1 minute 4ul of 0.7 mg per ml Ndc80 bonsai added, 1 minute manually blotted, then another 4ul of Ndc80 applied 1 minute 2ul removed with pipetter ...Method: 2ul of 0.25 mg per ml MTs applied to grid for 1 minute 4ul of 0.7 mg per ml Ndc80 bonsai added, 1 minute manually blotted, then another 4ul of Ndc80 applied 1 minute 2ul removed with pipetter Blot for 2 seconds before plunging, 0mm offset |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Mar 12, 2009 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.2 mm Astigmatism: objective lens astigmatism corrected at 100Kx mag Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: side-entry / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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3D reconstruction | Method: IRSHR / Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF Details: Particles were initially aligned using IHRSR protocol in SPIDER with naked MT as reference. Final reconstruction and CTF correction was performed with FREALIGN. A B-factor of -450 was ...Details: Particles were initially aligned using IHRSR protocol in SPIDER with naked MT as reference. Final reconstruction and CTF correction was performed with FREALIGN. A B-factor of -450 was applied with BFACTOR. FSC was calculated only for MT and Ndc80-NUF2 head, disordered outer head was excluded with soft mask. Symmetry type: HELICAL | ||||||||||||||||||||||||||||||
Atomic model building |
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Atomic model building | Source name: PDB / Type: experimental model
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Refinement step | Cycle: LAST
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