+Open data
-Basic information
Entry | Database: PDB / ID: 8g0p | |||||||||
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Title | Crystal structure of the human Ndc80:Nuf2 loop region | |||||||||
Components |
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Keywords | CELL CYCLE / Cell division / chromosome segregation / kinetochore / Ndc80 complex / Ndc80 / Nuf2 / loop / hinge / human | |||||||||
Function / homology | Function and homology information G2/MI transition of meiotic cell cycle / kinetochore adaptor activity / skeletal muscle satellite cell proliferation / 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 / outer kinetochore ...G2/MI transition of meiotic cell cycle / kinetochore adaptor activity / skeletal muscle satellite cell proliferation / 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 / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / spindle assembly involved in female meiosis I / mitotic spindle assembly checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / centrosome duplication / chromosome, centromeric region / 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 / cyclin binding / mitotic spindle organization / chromosome segregation / RHO GTPases Activate Formins / regulation of protein stability / kinetochore / Separation of Sister Chromatids / mitotic cell cycle / microtubule binding / cell division / centrosome / protein-containing complex binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Zahm, J.A. / Jenni, S. / Harrison, S.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Open Biology / Year: 2023 Title: Structure of the Ndc80 complex and its interactions at the yeast kinetochore-microtubule interface. Authors: Zahm, J.A. / Jenni, S. / Harrison, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g0p.cif.gz | 182.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g0p.ent.gz | 125.2 KB | Display | PDB format |
PDBx/mmJSON format | 8g0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/8g0p ftp://data.pdbj.org/pub/pdb/validation_reports/g0/8g0p | HTTPS FTP |
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-Related structure data
Related structure data | 8g0qC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16652.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NDC80, HEC, HEC1, KNTC2 / Production host: Escherichia coli (E. coli) / References: UniProt: O14777 |
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#2: Protein | Mass: 11567.251 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUF2, CDCA1, NUF2R / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZD4 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% (w/v) polyethylene glycol 4000, 0.1 M TRIS pH 8.6, and 0.2 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→40.75 Å / Num. obs: 36742 / % possible obs: 98.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 47.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.05 / Rrim(I) all: 0.132 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.84→1.87 Å / Redundancy: 5.7 % / Rmerge(I) obs: 4.03 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1005 / CC1/2: 0.33 / Rpim(I) all: 1.82 / Rrim(I) all: 4.44 / % possible all: 84.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.75 Å / SU ML: 0.3084 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.4717 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40.75 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -15.5160948454 Å / Origin y: 3.20932480929 Å / Origin z: 29.4258775818 Å
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Refinement TLS group | Selection details: all |