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Yorodumi- PDB-2p4n: Human Monomeric Kinesin (1BG2) and Bovine Tubulin (1JFF) Docked i... -
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-Basic information
Entry | Database: PDB / ID: 2p4n | ||||||
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Title | Human Monomeric Kinesin (1BG2) and Bovine Tubulin (1JFF) Docked into the 9-Angstrom Cryo-EM Map of Nucleotide-Free Kinesin Complexed to the Microtubule | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Motor protein / ATPase | ||||||
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 / natural killer cell mediated cytotoxicity / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / stress granule disassembly / positive regulation of axon guidance / mitochondrion transport along microtubule / ciliary rootlet / centrosome localization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / synaptic vesicle transport / Insulin processing / microtubule-based movement / microtubule-based process / centriolar satellite / axon cytoplasm / MHC class II antigen presentation / dendrite cytoplasm / phagocytic vesicle / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / axon guidance / structural constituent of cytoskeleton / cellular response to type II interferon / microtubule cytoskeleton organization / microtubule cytoskeleton / Signaling by ALK fusions and activated point mutants / nervous system development / mitotic cell cycle / microtubule binding / microtubule / vesicle / hydrolase activity / 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: 9 Å | ||||||
Authors | Sindelar, C.V. / Downing, K.H. | ||||||
Citation | Journal: J Cell Biol / Year: 2007 Title: The beginning of kinesin's force-generating cycle visualized at 9-A resolution. Authors: Charles V Sindelar / Kenneth H Downing / Abstract: We have used cryo-electron microscopy of kinesin-decorated microtubules to resolve the structure of the motor protein kinesin's crucial nucleotide response elements, switch I and the switch II helix, ...We have used cryo-electron microscopy of kinesin-decorated microtubules to resolve the structure of the motor protein kinesin's crucial nucleotide response elements, switch I and the switch II helix, in kinesin's poorly understood nucleotide-free state. Both of the switch elements undergo conformational change relative to the microtubule-free state. The changes in switch I suggest a role for it in "ejecting" adenosine diphosphate when kinesin initially binds to the microtubule. The switch II helix has an N-terminal extension, apparently stabilized by conserved microtubule contacts, implying a microtubule activation mechanism that could convey the state of the bound nucleotide to kinesin's putative force-delivering element (the "neck linker"). In deriving this structure, we have adapted an image-processing technique, single-particle reconstruction, for analyzing decorated microtubules. The resulting reconstruction visualizes the asymmetric seam present in native, 13-protofilament microtubules, and this method will provide an avenue to higher-resolution characterization of a variety of microtubule- binding proteins, as well as the microtubule itself. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2p4n.cif.gz | 249.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p4n.ent.gz | 193.1 KB | Display | PDB format |
PDBx/mmJSON format | 2p4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p4n_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2p4n_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2p4n_validation.xml.gz | 53.8 KB | Display | |
Data in CIF | 2p4n_validation.cif.gz | 77.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/2p4n ftp://data.pdbj.org/pub/pdb/validation_reports/p4/2p4n | HTTPS FTP |
-Related structure data
Related structure data | 1340MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules KAB
#1: Protein | Mass: 36405.070 Da / Num. of mol.: 1 / Fragment: K349 Construct of Human Kinesin / Source method: isolated from a natural source Details: The actual construct used in the EM studies is a mutant protein (called cys-lite) Source: (natural) Homo sapiens (human) / References: UniProt: P33176*PLUS |
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#2: Protein | Mass: 50121.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02550*PLUS |
#3: Protein | Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856*PLUS |
-Non-polymers , 6 types, 7 molecules
#4: Chemical | #5: Chemical | ChemComp-ADP / | #6: Chemical | ChemComp-ZN / | #7: Chemical | ChemComp-GTP / | #8: Chemical | ChemComp-GDP / | #9: Chemical | ChemComp-TA1 / | |
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-Details
Sequence details | THE SEQUENCE OF KINESIN (CHAIN K) IN THE SAMPLE INCLUDED MUTATIONS.THE CONSTRUCT IS KNOWN AS CYS- ...THE SEQUENCE OF KINESIN (CHAIN K) IN THE SAMPLE INCLUDED MUTATIONS.THE CONSTRUCT IS KNOWN AS CYS-LITE. MODEL CRYSTAL STRUCTURE FOR FITTING THE MAP WAS THE NATIVE SEQUENCE. IN THE CASE OF TUBULIN A AND B (CHAINS A AND B), THE SEQUENCE IN THE SAMPLE WAS DERIVED FROM COW, WHILE THE MODEL USED FOR FITTING THE MAP WAS A PIG PROTEIN. |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Buffer solution | pH: 6.8 | |||||||||||||||||||||||||
Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: 300 mesh copper grid | |||||||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL 4000 |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 400 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Cs: 4.1 mm |
Specimen holder | Temperature: 103.15 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 16 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: CTF correction was integrated into the back projection process with a customized C program | |||||||||||||||||||||
3D reconstruction | Method: Back projection with integrated CTF correction / Resolution: 9 Å / Num. of particles: 150000 / Nominal pixel size: 1 Å / Actual pixel size: 0.98 Å Magnification calibration: The magnification was calibrated by assuming a microtubule dimer spacing of 80.0 Angstroms. Details: Single-particle analysis was employed. / Symmetry type: HELICAL | |||||||||||||||||||||
Atomic model building | Space: RECIPROCAL | |||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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