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- PDB-4uxt: Conserved mechanisms of microtubule-stimulated ADP release, ATP b... -
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Basic information
Entry | Database: PDB / ID: 4uxt | ||||||
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Title | Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins | ||||||
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![]() | TRANSPORT PROTEIN | ||||||
Function / homology | ![]() anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / positive regulation of axon guidance / COPI-dependent Golgi-to-ER retrograde traffic / ciliary rootlet / kinesin complex ...anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / positive regulation of axon guidance / COPI-dependent Golgi-to-ER retrograde traffic / ciliary rootlet / kinesin complex / synaptic vesicle transport / Insulin processing / microtubule-based movement / cytoskeletal motor activity / kinesin binding / microtubule-based process / vesicle-mediated transport / axon cytoplasm / MHC class II antigen presentation / dendrite cytoplasm / axon guidance / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / nervous system development / microtubule binding / chemical synaptic transmission / perikaryon / microtubule / protein heterodimerization activity / GTPase activity / synapse / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.4 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C | ||||||
![]() | Atherton, J. / Farabella, I. / Yu, I.M. / Rosenfeld, S.S. / Houdusse, A. / Topf, M. / Moores, C. | ||||||
![]() | ![]() Title: Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins. Authors: Joseph Atherton / Irene Farabella / I-Mei Yu / Steven S Rosenfeld / Anne Houdusse / Maya Topf / Carolyn A Moores / ![]() ![]() ![]() Abstract: Kinesins are a superfamily of microtubule-based ATP-powered motors, important for multiple, essential cellular functions. How microtubule binding stimulates their ATPase and controls force generation ...Kinesins are a superfamily of microtubule-based ATP-powered motors, important for multiple, essential cellular functions. How microtubule binding stimulates their ATPase and controls force generation is not understood. To address this fundamental question, we visualized microtubule-bound kinesin-1 and kinesin-3 motor domains at multiple steps in their ATPase cycles--including their nucleotide-free states--at ∼ 7 Å resolution using cryo-electron microscopy. In both motors, microtubule binding promotes ordered conformations of conserved loops that stimulate ADP release, enhance microtubule affinity and prime the catalytic site for ATP binding. ATP binding causes only small shifts of these nucleotide-coordinating loops but induces large conformational changes elsewhere that allow force generation and neck linker docking towards the microtubule plus end. Family-specific differences across the kinesin-microtubule interface account for the distinctive properties of each motor. Our data thus provide evidence for a conserved ATP-driven mechanism for kinesins and reveal the critical mechanistic contribution of the microtubule interface. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 65.1 KB | Display | ![]() |
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PDB format | ![]() | 34.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2769MC ![]() 2765C ![]() 2766C ![]() 2767C ![]() 2768C ![]() 2770C ![]() 2771C ![]() 4uxoC ![]() 4uxpC ![]() 4uxrC ![]() 4uxsC ![]() 4uxyC ![]() 4uy0C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 50107.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 38030.184 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, UNP RESIDUES 1-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 5 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/TA1.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/TA1.gif)
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-GTP / |
#7: Chemical | ChemComp-GDP / |
#8: Chemical | ChemComp-TA1 / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 13-PROTOFILAMENT MICROTUBULE-BOUND HUMAN KINESIN-1 MOTOR DOMAIN IN ABSENCE OF NUCLEOTIDES Type: COMPLEX |
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Buffer solution | Name: 20MM PIPES, 2MM MGCL2, 1MM EGTA, 2MM DTT, 10 U/ML APYRASE pH: 6.8 Details: 20MM PIPES, 2MM MGCL2, 1MM EGTA, 2MM DTT, 10 U/ML APYRASE |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: LIQUID ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Dec 10, 2012 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 100000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 400 nm / Cs: 2.3 mm |
Specimen holder | Temperature: 90 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 497 |
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Processing
EM software |
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CTF correction | Details: FREALIGN | |||||||||||||||
3D reconstruction | Resolution: 7.4 Å / Num. of particles: 168974 / Actual pixel size: 1.5 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2769. (DEPOSITION ID: 12602). Symmetry type: HELICAL | |||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY | |||||||||||||||
Atomic model building | PDB-ID: 1BG2 Accession code: 1BG2 / Source name: PDB / Type: experimental model | |||||||||||||||
Refinement | Highest resolution: 7.4 Å | |||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 7.4 Å
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