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- PDB-8qau: Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex -

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Basic information

Entry
Database: PDB / ID: 8qau
TitleOuter kinetochore Ndc80-Dam1 alpha/beta-tubulin complex
Components
  • (Kinetochore protein ...) x 2
  • DASH complex subunit DAM1
  • Tubulin alpha-1A chain
  • Tubulin beta chain
KeywordsCELL CYCLE / Kinetochore / microtubule / error correction / chromosome segregation
Function / homology
Function and homology information


mitotic spindle polar microtubule / Ndc80 complex / DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / kinetochore organization / positive regulation of attachment of spindle microtubules to kinetochore / meiotic chromosome segregation / mitotic spindle pole body / attachment of spindle microtubules to kinetochore ...mitotic spindle polar microtubule / Ndc80 complex / DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / kinetochore organization / positive regulation of attachment of spindle microtubules to kinetochore / meiotic chromosome segregation / mitotic spindle pole body / attachment of spindle microtubules to kinetochore / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / spindle pole body / protein localization to kinetochore / positive regulation of microtubule polymerization / mitotic spindle organization / chromosome segregation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spindle microtubule / structural constituent of cytoskeleton / mitotic spindle / kinetochore / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / cell division / GTPase activity / protein-containing complex binding / GTP binding / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DASH complex subunit Dam1 / DASH complex subunit Dam1 / Kinetochore protein Nuf2, N-terminal / Nuf2, N-terminal domain superfamily / Nuf2 family / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / HEC/Ndc80p family / Domain of unknown function (DUF5595) ...DASH complex subunit Dam1 / DASH complex subunit Dam1 / Kinetochore protein Nuf2, N-terminal / Nuf2, N-terminal domain superfamily / Nuf2 family / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / HEC/Ndc80p family / Domain of unknown function (DUF5595) / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Tubulin alpha-1A chain / Tubulin beta chain / Kinetochore protein NUF2 / Kinetochore protein NDC80 / DASH complex subunit DAM1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsMuir, K.W. / Barford, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: Biorxiv / Year: 2023
Title: Mechanism of outer kinetochore assembly on microtubules and its regulation by mitotic error correction
Authors: Muir, K.W. / Batters, C. / Dendooven, T. / Yang, J. / Zhang, Z. / Burt, A. / Barford, D.
History
DepositionAug 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Tubulin alpha-1A chain
D: Tubulin beta chain
A: Kinetochore protein NDC80
B: Kinetochore protein NUF2
E: DASH complex subunit DAM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,9879
Polymers272,1425
Non-polymers1,8454
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 3 molecules CDE

#1: Protein Tubulin alpha-1A chain


Mass: 50121.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02550
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#5: Protein DASH complex subunit DAM1


Mass: 38477.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DAM1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53267

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Kinetochore protein ... , 2 types, 2 molecules AB

#3: Protein Kinetochore protein NDC80


Mass: 80609.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NDC80 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P40460
#4: Protein Kinetochore protein NUF2


Mass: 53025.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NUF2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P33895

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Non-polymers , 4 types, 4 molecules

#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#9: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Outer kinetochore Ndc80-Nuf2 CH domains bound to Dam1 in complex with alpha-beta tubulin
Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95730 / Symmetry type: POINT
Atomic model buildingB value: 540.98 / Protocol: OTHER / Space: REAL
Details: Initial rigid body fitting was performed in chimera, with manual correction in coot and real-space refinement in PHENIX
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410342
ELECTRON MICROSCOPYf_angle_d0.67314083
ELECTRON MICROSCOPYf_dihedral_angle_d7.4551472
ELECTRON MICROSCOPYf_chiral_restr0.0421588
ELECTRON MICROSCOPYf_plane_restr0.0051848

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