[English] 日本語
Yorodumi- PDB-6ojq: Monomeric kinesin-1 motor domain in no-nucleotide state bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ojq | ||||||
---|---|---|---|---|---|---|---|
Title | Monomeric kinesin-1 motor domain in no-nucleotide state bound to GMPCPP-stabilized microtubule | ||||||
Components |
| ||||||
Keywords | MOTOR PROTEIN / Kinesin / Microtubule | ||||||
Function / homology | Function and homology information cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization ...cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / stress granule disassembly / positive regulation of axon guidance / mitochondrion transport along microtubule / centrosome localization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / ciliary rootlet / natural killer cell mediated cytotoxicity / kinesin complex / synaptic vesicle transport / Insulin processing / microtubule-based movement / microtubule-based process / centriolar satellite / axon cytoplasm / phagocytic vesicle / MHC class II antigen presentation / dendrite cytoplasm / positive regulation of protein localization to plasma membrane / regulation of membrane potential / axon guidance / positive regulation of synaptic transmission, GABAergic / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / cellular response to type II interferon / microtubule cytoskeleton organization / microtubule cytoskeleton / Signaling by ALK fusions and activated point mutants / mitotic cell cycle / nervous system development / microtubule binding / vesicle / microtubule / cadherin binding / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å | ||||||
Authors | Cha, H.K. / Debs, G. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Structural Intermediates of the Dimeric Kinesin Stepping Cycle Revealed by Cryo-EM Authors: Cha, H.K. / Debs, G. / Liu, X. / Liu, D. / Sindelar, C.V. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ojq.cif.gz | 417.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ojq.ent.gz | 332.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ojq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ojq_validation.pdf.gz | 915.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ojq_full_validation.pdf.gz | 923.7 KB | Display | |
Data in XML | 6ojq_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 6ojq_validation.cif.gz | 56.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/6ojq ftp://data.pdbj.org/pub/pdb/validation_reports/oj/6ojq | HTTPS FTP |
-Related structure data
Related structure data | 20092MC 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 BAK
#1: Protein | Mass: 47825.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856 |
---|---|
#2: Protein | Mass: 48665.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947 |
#3: Protein | Mass: 35445.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF5B, KNS, KNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33176 |
-Non-polymers , 3 types, 4 molecules
#4: Chemical | ChemComp-G2P / | ||
---|---|---|---|
#5: Chemical | #6: Chemical | ChemComp-GTP / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Monomeric kinesin-1 motor domain in the no-nucleotide state bound to GMPCPP-stabilized microtubules Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
---|---|
Source (natural) | Organism: Bos taurus (cattle) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | 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 |
Image recording | Electron dose: 1.625 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 403424 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library | ||||||||||||||||||||||||
Refine LS restraints |
|