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- PDB-5nd7: Microtubule-bound MKLP2 motor domain in the presence of AMPPNP -

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Basic information

Entry
Database: PDB / ID: 5nd7
TitleMicrotubule-bound MKLP2 motor domain in the presence of AMPPNP
Components
  • Kinesin-like protein KIF20AKIF20A
  • Tubulin alpha chain
  • Tubulin beta-2B chain
KeywordsMOTOR PROTEIN / Kinesin Mitosis Microtubules / Motor protein
Function / homologyTubulin, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Regulation of PLK1 Activity at G2/M Transition / Tubulin / Kinesin motor domain / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site ...Tubulin, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Regulation of PLK1 Activity at G2/M Transition / Tubulin / Kinesin motor domain / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Kinesin motor domain, conserved site / Kinesin-like protein KIF20A / Kinesin-like protein / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Tubulin/FtsZ, GTPase domain superfamily / Kinesin motor domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ family, GTPase domain / Kinesin motor domain / Tubulin C-terminal domain / Tubulin subunits alpha, beta, and gamma signature. / Tubulin-beta mRNA autoregulation signal. / Kinesin motor domain signature. / Kinesin motor domain profile. / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / RHO GTPases Activate Formins / Mitotic Telophase/Cytokinesis / COPI-dependent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / Kinesins / Carboxyterminal post-translational modifications of tubulin / AURKA Activation by TPX2 / The role of GTSE1 in G2/M progression after G2 checkpoint / Mitotic Prometaphase / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Recruitment of mitotic centrosome proteins and complexes / Kinesins / Hedgehog 'on' state / RHO GTPases activate IQGAPs / Intraflagellar transport / Anchoring of the basal body to the plasma membrane / Cilium Assembly / Hedgehog 'off' state / Recycling pathway of L1 / Recruitment of NuMA to mitotic centrosomes / cell separation after cytokinesis / microtubule bundle formation / positive regulation of axon guidance / kinesin complex / cleavage furrow / cytoplasmic microtubule / cellular response to interleukin-4 / recycling endosome / mitotic cytokinesis / microtubule-based process / intercellular bridge / microtubule cytoskeleton organization / microtubule motor activity / cytoplasmic ribonucleoprotein granule / microtubule-based movement / neuron migration / structural constituent of cytoskeleton / regulation of cytokinesis / microtubule cytoskeleton / spindle / double-stranded RNA binding / midbody / protein transport / microtubule / microtubule binding / ATPase activity / GTPase activity / myelin sheath / GTP binding / ubiquitin protein ligase binding / protein kinase binding / protein heterodimerization activity / Golgi apparatus / nucleoplasm / ATP binding / cytosol / cytoplasm / Tubulin alpha chain / Tubulin alpha-1B chain / Kinesin-like protein KIF20A / Tubulin beta-2B chain
Function and homology information
Specimen sourceMus musculus (house mouse)
Bos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.9 Å resolution
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.
CitationJournal: Elife / Year: 2017
Title: The divergent mitotic kinesin MKLP2 exhibits atypical structure and mechanochemistry.
Authors: 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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Assembly

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)158,4119
Polyers156,0363
Non-polymers2,3756
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)9950
ΔGint (kcal/M)-59
Surface area (Å2)44070
MethodPISA
Conformers5 models

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Components

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Protein/peptide , 3 types, 3 molecules CAB

#1: Protein/peptide Kinesin-like protein KIF20A / 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 (house mouse) / Gene: Kif20a, Rab6kifl / Production host: Escherichia coli (E. coli) / References: UniProt: P97329
#2: Protein/peptide Tubulin alpha chain


Mass: 50107.238 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: F2Z4C1, UniProt: P81947*PLUS
#3: Protein/peptide Tubulin beta-2B chain


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

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Non-polymers , 5 types, 6 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Formula: C10H17N6O12P3 / Comment: AMP-PNP (energy-carrying molecule analogue) *YM
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


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


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: single particle reconstruction

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Sample preparation

Component

Details: Microtubule bound to taxol / Type: COMPLEX

IDNameEntity IDParent IDSource
1Complex of 13pf microtubule with bound MKLP2 motor domain in the presence of AMPPNP1, 2, 30MULTIPLE SOURCES
2Kinesin-like protein KIF20A11RECOMBINANT
3Tubulin alpha and beta chains2, 31NATURAL
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
1110090Mus musculus (house mouse)
229913Bos taurus (cattle)
Source (recombinant)Organism: Escherichia coli (E. coli)
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: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 10858
Details: Gold-standard FSCtrue using noise substitution test (Chen et al., 2014)
Symmetry type: POINT

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