[English] 日本語
Yorodumi- PDB-6wwr: Kif14[391-743] - ADP-AlFx open state class in complex with a micr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wwr | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Kif14[391-743] - ADP-AlFx open state class in complex with a microtubule | |||||||||||||||||||||||||||
Components |
| |||||||||||||||||||||||||||
Keywords | MOTOR PROTEIN / KIF14 / kinesin / motility / microtubule / tubulin | |||||||||||||||||||||||||||
Function / homology | Function and homology information cerebellar granular layer structural organization / regulation of cell maturation / cerebellar Purkinje cell layer structural organization / RHO GTPases activate CIT / negative regulation of integrin activation / RND2 GTPase cycle / RND1 GTPase cycle / cell proliferation in forebrain / regulation of Rap protein signal transduction / cerebellar cortex development ...cerebellar granular layer structural organization / regulation of cell maturation / cerebellar Purkinje cell layer structural organization / RHO GTPases activate CIT / negative regulation of integrin activation / RND2 GTPase cycle / RND1 GTPase cycle / cell proliferation in forebrain / regulation of Rap protein signal transduction / cerebellar cortex development / olfactory bulb development / 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 / Flemming body / plus-end-directed microtubule motor activity / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / microtubule motor activity / regulation of myelination / kinesin complex / mitotic metaphase chromosome alignment / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / activation of protein kinase activity / microtubule-based movement / positive regulation of cytokinesis / regulation of G1/S transition of mitotic cell cycle / spindle midzone / regulation of cell adhesion / regulation of neuron apoptotic process / regulation of G2/M transition of mitotic cell cycle / regulation of cell migration / tubulin binding / substrate adhesion-dependent cell spreading / hippocampus development / regulation of cell growth / PDZ domain binding / establishment of protein localization / structural constituent of cytoskeleton / cerebral cortex development / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / midbody / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / microtubule / cell division / GTPase activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / GTP binding / protein kinase binding / ATP hydrolysis activity / ATP binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Mus musculus (house mouse) Sus scrofa (pig) | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||||||||||||||||||||
Authors | Benoit, M.P.M.H. / Asenjo, A.B. / Paydar, M. / Dhakal, S. / Kwok, B. / Sosa, H. | |||||||||||||||||||||||||||
Funding support | United States, Canada, 8items
| |||||||||||||||||||||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis of mechano-chemical coupling by the mitotic kinesin KIF14. Authors: Matthieu P M H Benoit / Ana B Asenjo / Mohammadjavad Paydar / Sabin Dhakal / Benjamin H Kwok / Hernando Sosa / Abstract: KIF14 is a mitotic kinesin whose malfunction is associated with cerebral and renal developmental defects and several cancers. Like other kinesins, KIF14 couples ATP hydrolysis and microtubule binding ...KIF14 is a mitotic kinesin whose malfunction is associated with cerebral and renal developmental defects and several cancers. Like other kinesins, KIF14 couples ATP hydrolysis and microtubule binding to the generation of mechanical work, but the coupling mechanism between these processes is still not fully clear. Here we report 20 high-resolution (2.7-3.9 Å) cryo-electron microscopy KIF14-microtubule structures with complementary functional assays. Analysis procedures were implemented to separate coexisting conformations of microtubule-bound monomeric and dimeric KIF14 constructs. The data provide a comprehensive view of the microtubule and nucleotide induced KIF14 conformational changes. It shows that: 1) microtubule binding, the nucleotide species, and the neck-linker domain govern the transition between three major conformations of the motor domain; 2) an undocked neck-linker prevents the nucleotide-binding pocket to fully close and dampens ATP hydrolysis; 3) 13 neck-linker residues are required to assume a stable docked conformation; 4) the neck-linker position controls the hydrolysis rather than the nucleotide binding step; 5) the two motor domains of KIF14 dimers adopt distinct conformations when bound to the microtubule; and 6) the formation of the two-heads-bound-state introduces structural changes in both motor domains of KIF14 dimers. These observations provide the structural basis for a coordinated chemo-mechanical kinesin translocation model. | |||||||||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wwr.cif.gz | 227.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6wwr.ent.gz | 176.9 KB | Display | PDB format |
PDBx/mmJSON format | 6wwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wwr_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6wwr_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6wwr_validation.xml.gz | 55.2 KB | Display | |
Data in CIF | 6wwr_validation.cif.gz | 80.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/6wwr ftp://data.pdbj.org/pub/pdb/validation_reports/ww/6wwr | HTTPS FTP |
-Related structure data
Related structure data | 21945MC 6wweC 6wwfC 6wwgC 6wwhC 6wwiC 6wwjC 6wwkC 6wwlC 6wwmC 6wwnC 6wwoC 6wwpC 6wwqC 6wwsC 6wwtC 6wwuC 6wwvC 7lvqC 7lvrC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 3 types, 3 molecules ABK
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / References: UniProt: Q2XVP4 |
---|---|
#2: Protein | Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / References: UniProt: A0A287AGU7 |
#3: Protein | Mass: 39751.730 Da / Num. of mol.: 1 / Fragment: UNP residues 391-743 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif14 / Production host: Escherichia coli (E. coli) / References: UniProt: L0N7N1 |
-Non-polymers , 5 types, 5 molecules
#4: Chemical | ChemComp-GTP / |
---|---|
#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-GDP / |
#7: Chemical | ChemComp-TA1 / |
#8: Chemical | ChemComp-ADP / |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||||||||||
Buffer solution | pH: 6.8 | ||||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil | ||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Calibrated magnification: 60606 X / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 70.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 168.07 ° / Axial rise/subunit: 5.44 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Details: manual picking of filaments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 348209 / Algorithm: FOURIER SPACE Details: 2 half datasets containing one distinct half of each filament were refined independently. Symmetry type: HELICAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |