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- PDB-5nd3: Microtubule-bound MKLP2 motor domain in the with no nucleotide -

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Database: PDB / ID: 5nd3
TitleMicrotubule-bound MKLP2 motor domain in the with no nucleotide
  • Kinesin-like protein KIF20A
  • Tubulin alpha chain
  • Tubulin beta-2B chain
KeywordsMOTOR PROTEIN / Kinesin Mitosis Microtubules / Motor protein
Specimen sourceMus musculus / mammal / House mouse (Wikipedia) /
Bos taurus / mammal / Cattle (Wikipedia) /
MethodElectron microscopy (6.1 Å resolution / Filament / Single particle)
AuthorsAtherton, J. / Yu, I.M. / Cook, A. / Muretta, J.M. / Joseph, A.P. / Major, J. / Sourigues, Y. / Clause, J. / Topf, M. / Rosenfeld, S.S. / Houdusse, A. / Moores, C.A.
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
The divergent mitotic kinesin MKLP2 exhibits atypical structure and mechanochemistry.
Joseph Atherton / I-Mei Yu / Alexander Cook / Joseph M Muretta / Agnel Joseph / Jennifer Major / Yannick Sourigues / Jeffrey Clause / Maya Topf / Steven S Rosenfeld / Anne Houdusse / Carolyn A Moores

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 7, 2017 / Release: Oct 4, 2017

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Deposited unit
C: Kinesin-like protein KIF20A
A: Tubulin alpha chain
B: Tubulin beta-2B chain
hetero molecules

Theoretical massNumber of molelcules
Total (without water)157,8817

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)9370
ΔGint (kcal/M)-50
Surface area (Å2)43610
Conformers5 models


Protein/peptide , 3 types, 3 molecules CAB

#1: Protein/peptide Kinesin-like protein KIF20A / Kinesin-like protein 174 / Rab6-interacting kinesin-like protein / Rabkinesin-6

Mass: 56021.332 Da / Num. of mol.: 1 / Source: (gene. exp.) Mus musculus / Gene: Kif20a, Rab6kifl / Production host: Escherichia coli / References: UniProt: P97329
#2: Protein/peptide Tubulin alpha chain

Mass: 50107.238 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: F2Z4C1
#3: Protein/peptide Tubulin beta-2B chain

Mass: 49907.770 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q6B856

Non-polymers , 4 types, 4 molecules


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Wikipedia: Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#5: Chemical ChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Wikipedia: Magnesium
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE

Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2 / Wikipedia: Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM
#7: Chemical ChemComp-TA1 / TAXOL

Mass: 853.906 Da / Num. of mol.: 1 / Formula: C47H51NO14

Experimental details


EM experimentAggregation state: FILAMENT / Reconstruction method: SINGLE PARTICLE

Sample preparation


Details: Microtubule bound to taxol and GDP / Type: COMPLEX

IDNameEntity IDParent IDSource
1Complex of 13pf taxol-GDP microtubule with bound MKLP2 motor domain with no-nucleotide1, 2, 30MULTIPLE SOURCES
2Kinesin-like protein KIF20A11RECOMBINANT
3Tubulin alpha and beta chains2, 31NATURAL
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
1210090Mus musculus
239913Bos taurus
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)


3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 9257
Details: Gold-standard FSCtrue using noise substitution test (Chen et al., 2014)
Symmetry type: POINT

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