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Yorodumi- PDB-7x4n: Crystal Structure of C. elegans kinesin-4 KLP-12 complexed with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x4n | ||||||||||||||||||
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Title | Crystal Structure of C. elegans kinesin-4 KLP-12 complexed with tubulin and DARPin | ||||||||||||||||||
Components |
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Keywords | MOTOR PROTEIN / kinesin-4 / KLP-12 / KIF21A / KIF21B / microtubule / tubulin / axon / CFEOM1 / DARPin | ||||||||||||||||||
Function / homology | Function and homology information COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / microtubule motor activity / kinesin complex / microtubule-based movement / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding ...COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / microtubule motor activity / kinesin complex / microtubule-based movement / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / GTPase activity / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | synthetic construct (others) Caenorhabditis elegans (invertebrata) Sus scrofa (pig) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å | ||||||||||||||||||
Authors | Taguchi, S. / Imasaki, T. / Saijo-Hamano, Y. / Sakai, N. / Nitta, R. | ||||||||||||||||||
Funding support | Japan, 5items
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Citation | Journal: Elife / Year: 2022 Title: Structural model of microtubule dynamics inhibition by kinesin-4 from the crystal structure of KLP-12 -tubulin complex. Authors: Taguchi, S. / Nakano, J. / Imasaki, T. / Kita, T. / Saijo-Hamano, Y. / Sakai, N. / Shigematsu, H. / Okuma, H. / Shimizu, T. / Nitta, E. / Kikkawa, S. / Mizobuchi, S. / Niwa, S. / Nitta, R. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x4n.cif.gz | 275.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x4n.ent.gz | 215 KB | Display | PDB format |
PDBx/mmJSON format | 7x4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x4n_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7x4n_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 7x4n_validation.xml.gz | 50.6 KB | Display | |
Data in CIF | 7x4n_validation.cif.gz | 67.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/7x4n ftp://data.pdbj.org/pub/pdb/validation_reports/x4/7x4n | HTTPS FTP |
-Related structure data
Related structure data | 5mioS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 4 molecules ABCE
#1: Protein | Mass: 50121.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02550 |
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#2: Protein | Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554 |
#3: Protein | Mass: 16792.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
#4: Protein | Mass: 40013.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: klp-12, CELE_T01G1.1, T01G1.1 / Production host: Escherichia coli (E. coli) / References: UniProt: G5EGS3 |
-Non-polymers , 4 types, 5 molecules
#5: Chemical | ChemComp-GTP / | ||||
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#6: Chemical | #7: Chemical | ChemComp-GDP / | #8: Chemical | ChemComp-ANP / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: ammonium acetate, HEPES, polyethylene glycol (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→50 Å / Num. obs: 34669 / % possible obs: 98.2 % / Redundancy: 87.1 % / CC1/2: 0.977 / Rrim(I) all: 0.355 / Net I/σ(I): 19.28 |
Reflection shell | Resolution: 2.88→3.05 Å / Mean I/σ(I) obs: 3.39 / Num. unique obs: 5455 / CC1/2: 0.513 / Rrim(I) all: 1.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MIO Resolution: 2.88→49.25 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.88→49.25 Å
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Refine LS restraints |
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LS refinement shell |
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