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Open data
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Basic information
Entry | Database: PDB / ID: 8utw | |||||||||||||||||||||
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Title | KIF1A[1-393] P305L mutant APO in complex with a microtubule | |||||||||||||||||||||
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![]() | MOTOR PROTEIN / KIF1A / kinesin / motility / microtubule / tubulin | |||||||||||||||||||||
Function / homology | ![]() neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state ...neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / neuronal dense core vesicle / cytoskeletal motor activity / vesicle-mediated transport / axon cytoplasm / 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 / microtubule binding / microtubule / axon / GTPase activity / synapse / dendrite / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||||||||
![]() | Benoit, M.P.M.H. / Rao, L. / Asenjo, A.B. / Gennerich, A. / Sosa, H. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM of human KIF1A reveals its mechanism of motility and the effect of its pathogenic variant P305L Authors: Benoit, M.P.M.H. / Rao, L. / Asenjo, A.B. / Gennerich, A. / Sosa, H. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257.4 KB | Display | ![]() |
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PDB format | ![]() | 198.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 54.1 KB | Display | |
Data in CIF | ![]() | 79.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 42552MC ![]() 8utnC ![]() 8utoC ![]() 8utpC ![]() 8utqC ![]() 8utrC ![]() 8utsC ![]() 8uttC ![]() 8utuC ![]() 8utvC ![]() 8utyC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 3 types, 3 molecules KAB
#1: Protein | Mass: 49304.480 Da / Num. of mol.: 1 / Fragment: residues 1-393 / Mutation: P305L Source method: isolated from a genetically manipulated source Details: "linker" residues are comprised of a leucine zipper based on S. cerevisiae GCN4, which is followed by the C-terminal strep-tag Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 4 types, 4 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/TA1.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/TA1.gif)
#4: Chemical | ChemComp-GTP / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-GDP / |
#7: Chemical | ChemComp-TA1 / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: KIF1A[1-393] P305L mutant APO in complex with a 15R microtubule Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Buffer solution | pH: 6.8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3010 nm / Nominal defocus min: 690 nm |
Image recording | Electron dose: 50.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
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Helical symmerty |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 620149 Details: NUMBER OF ASYMMETRIC UNITS USED IS REPORTED IN "NUMBER OF SEGMENTS USED", DUE TO THE LOCAL PROCESSING STRATEGY EMPLOYED. Symmetry type: HELICAL | |||||||||||||||
Refinement | Highest resolution: 3.4 Å |