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- PDB-5nd4: Microtubule-bound MKLP2 motor domain in the presence of ADP.AlFx -

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Database: PDB / ID: 5nd4
TitleMicrotubule-bound MKLP2 motor domain in the presence of ADP.AlFx
DescriptorKinesin-like protein KIF20A
Tubulin alpha chain
Tubulin beta-2B chain
KeywordsMOTOR PROTEIN / Kinesin / Mitosis / Microtubules / Motor protein
Specimen sourceMus musculus / mammal / House Mouse / ハツカネズミ, はつかねずみ /
Bos taurus / mammal / Bovine / ウシ /
MethodElectron microscopy (4.4 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)152,19010

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)11080
ΔGint (kcal/M)-67
Surface area (Å2)43780


Polypeptide(L) , 3 types, 3 molecules CAB

#1: Polypeptide(L)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 / References: UniProt: P97329

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)Tubulin alpha chain

Mass: 45959.980 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: F2Z4C1
#3: Polypeptide(L)Tubulin beta-2B chain

Mass: 47809.746 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q6B856

Cellular component

Molecular function

Biological process

Non-polymers , 6 types, 7 molecules


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2
#5: ChemicalChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg

Mass: 102.975 Da / Num. of mol.: 1 / Formula: AlF4

Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3

Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2
#9: ChemicalChemComp-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 / Type: COMPLEX

IDNameEntity IDParent IDSource
1Complex of 14pf microtubule with bound MKLP2 motor domain in the presence of ADP.AlFx1, 2, 30MULTIPLE SOURCES
2Tubulin alpha and beta chains2, 31NATURAL
3Kinesin-like protein KIF20A11RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129913Bos taurus
2310090Mus musculus
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: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 21239
Details: Gold-standard FSCtrue using noise substitution test (Chen et al., 2014)
Symmetry type: POINT

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