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- PDB-4ck7: Pseudo-atomic model of microtubule-bound human kinesin-5 motor do... -

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Basic information

Entry
Database: PDB / ID: 4ck7
TitlePseudo-atomic model of microtubule-bound human kinesin-5 motor domain in presence of adp.alfx (NECK-LINKER IN ITS DISCONNECTED CONFORMATION, based on cryo-electron microscopy experiment
Components
  • KINESIN-LIKE PROTEIN KIF11
  • TUBULIN ALPHA-1D CHAIN
  • TUBULIN BETA-2B CHAIN
KeywordsMOTOR PROTEIN / KINESINS / MICROTUBULES / MITOSIS / MECHANOCHEMISTRY
Function / homologyKinesin motor domain, conserved site / Tubulin/FtsZ family, GTPase domain / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / RHO GTPases activate IQGAPs / Tubulin, C-terminal ...Kinesin motor domain, conserved site / Tubulin/FtsZ family, GTPase domain / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / RHO GTPases activate IQGAPs / Tubulin, C-terminal / Kinesin-associated microtubule-binding domain / P-loop containing nucleoside triphosphate hydrolase / Kinesin-like protein / Tubulin/FtsZ, GTPase domain superfamily / Kinesin motor domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Kinesin motor domain / Kinesin motor domain / Tubulin C-terminal domain / Kinesin-associated microtubule-binding / 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 / Separation of Sister Chromatids / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Recruitment of NuMA to mitotic centrosomes / Recycling pathway of L1 / Hedgehog 'off' state / Alpha tubulin / Tubulin / Intraflagellar transport / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / Kinesins / Carboxyterminal post-translational modifications of tubulin / The role of GTSE1 in G2/M progression after G2 checkpoint / Mitotic Prometaphase / Cilium Assembly / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / Hedgehog 'on' state / RHO GTPases Activate Formins / ATP-dependent microtubule motor activity, plus-end-directed / positive regulation of axon guidance / regulation of mitotic centrosome separation / mitotic centrosome separation / kinesin complex / retrograde vesicle-mediated transport, Golgi to ER / mitotic spindle assembly / microtubule-based process / spindle organization / antigen processing and presentation of exogenous peptide antigen via MHC class II / microtubule motor activity / mitotic spindle organization / mitotic spindle / microtubule-based movement / neuron migration / structural constituent of cytoskeleton / chromosome segregation / microtubule cytoskeleton / spindle / mitotic cell cycle / spindle pole / protein-containing complex binding / microtubule / microtubule binding / GTPase activity / cell division / GTP binding / protein kinase binding / protein heterodimerization activity / membrane / ATP binding / cytosol / cytoplasm / Kinesin-like protein KIF11 / Tubulin alpha-1D chain / Tubulin beta-2B chain
Function and homology information
Specimen sourceHOMO SAPIENS (human)
BOS TAURUS (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9.2 Å resolution
Model type detailsCA ATOMS ONLY, CHAIN A, B, C
AuthorsGoulet, A. / Major, J. / Jun, Y. / Gross, S. / Rosenfeld, S. / Moores, C.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Comprehensive structural model of the mechanochemical cycle of a mitotic motor highlights molecular adaptations in the kinesin family.
Authors: Adeline Goulet / Jennifer Major / Yonggun Jun / Steven P Gross / Steven S Rosenfeld / Carolyn A Moores
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 30, 2013 / Release: Feb 5, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 5, 2014Structure modelrepositoryInitial release
1.1Feb 19, 2014Structure modelDatabase references
1.2Aug 30, 2017Structure modelData collection / Refinement descriptionem_3d_fitting / em_software_em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-2533
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUBULIN ALPHA-1D CHAIN
B: TUBULIN BETA-2B CHAIN
C: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,19710
Polyers141,8173
Non-polymers2,3807
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

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Components

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Protein/peptide , 3 types, 3 molecules ABC

#1: Protein/peptide TUBULIN ALPHA-1D CHAIN / ALPHA TUBULIN / Coordinate model: Cα atoms only


Mass: 50236.352 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS (cattle) / Organ: BRAIN / References: UniProt: Q2HJ86
#2: Protein/peptide TUBULIN BETA-2B CHAIN / BETA TUBULIN / Coordinate model: Cα atoms only


Mass: 49907.770 Da / Num. of mol.: 1 / Source: (natural) BOS TAURUS (cattle) / Organ: BRAIN / References: UniProt: Q6B856
#3: Protein/peptide KINESIN-LIKE PROTEIN KIF11 / KINESIN-LIKE PROTEIN 1 / KINESIN-LIKE SPINDLE PROTEIN HKSP / KINESIN-RELATED MOTOR PROTEIN EG5 / THYROID RECEPTOR-INTERACTING PROTEIN 5 / TR-INTERACTING PROTEIN 5 / TRIP-5 / KINESIN-5 / Coordinate model: Cα atoms only


Mass: 41673.105 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 1-367 / Mutation: YES / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid name: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P52732

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Non-polymers , 6 types, 7 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


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


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


Mass: 853.906 Da / Num. of mol.: 1 / Formula: C47H51NO14 / Paclitaxel
#8: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Formula: AlF3 / Aluminium fluoride
#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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Details

Sequence detailsCYS-LITE MUTANT CONTAINING THE SUBSTITUTION T126C

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: MICROTUBULE-BOUND HUMAN KINESIN-5 MOTOR DOMAIN / Type: COMPLEX
Buffer solutionName: 80 MM PIPES 5 MM MGCL2 1 MM EGTA 1 MM TCEP / Details: 80 MM PIPES 5 MM MGCL2 1 MM EGTA 1 MM TCEP / pH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20 / Date: Mar 10, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 2 mm
Specimen holderTemperature: 90 kelvins
Image recordingElectron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 125

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Processing

EM software
IDNameCategory
1Flex-EMmodel fitting
2UCSF Chimeramodel fitting
3FREALIGN3D reconstruction
4SPIDER3D reconstruction
CTF correctionDetails: FREALIGN
SymmetryPoint symmetry: C1
3D reconstructionResolution: 9.2 Å / Number of particles: 10692
Details: THE N-TERMINAL SEQUENCE WAS MODELLED USING MODELLER. THE DISCONNECTED CONFORMATION OF THE NECK-LINKER WAS CALCULATED USING A CONJUGATE-GRADIENT ENERGY MINIMIZATION. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2533. (DEPOSITION ID: 12198).
Symmetry type: POINT
Atomic model buildingDetails: METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY / Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient
Atomic model building
IDPDB-ID 3D fitting ID
13HQD1
21JFF1
Least-squares processHighest resolution: 9.2 Å
Refine hist #LASTHighest resolution: 9.2 Å
Number of atoms included #LASTProtein: 1199 / Nucleic acid: 0 / Ligand: 155 / Solvent: 0 / Total: 1354

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