+Open data
-Basic information
Entry | Database: PDB / ID: 7ol3 | ||||||
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Title | Human ATL1 N417ins (catalytic core) | ||||||
Components | Atlastin-1 | ||||||
Keywords | MEMBRANE PROTEIN / Dynamin-related protein / membrane fusion / endoplasmic reticulum | ||||||
Function / homology | Function and homology information endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / Golgi cis cisterna / endoplasmic reticulum tubular network / endoplasmic reticulum organization / axonogenesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / Golgi membrane / axon ...endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / Golgi cis cisterna / endoplasmic reticulum tubular network / endoplasmic reticulum organization / axonogenesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / Golgi membrane / axon / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / endoplasmic reticulum / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kelly, C.M. / Sondermann, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: A novel insertion mutation in atlastin 1 is associated with spastic quadriplegia, increased membrane tethering, and aberrant conformational switching. Authors: Kelly, C.M. / Zeiger, P.J. / Narayanan, V. / Ramsey, K. / Sondermann, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ol3.cif.gz | 382.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ol3.ent.gz | 295.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ol3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ol3_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7ol3_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7ol3_validation.xml.gz | 41 KB | Display | |
Data in CIF | 7ol3_validation.cif.gz | 63 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/7ol3 ftp://data.pdbj.org/pub/pdb/validation_reports/ol/7ol3 | HTTPS FTP |
-Related structure data
Related structure data | 4idqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52615.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATL1, GBP3, SPG3A / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8WXF7, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.48 Å3/Da / Density % sol: 50.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl pH 8.1, 2% Tacsimate pH 8, 18% PEG 3,350, 25% Glycerol (cryo-protection) |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.43 Å / Num. obs: 82941 / % possible obs: 99.75 % / Redundancy: 7.3 % / Biso Wilson estimate: 21.59 Å2 / CC1/2: 0.992 / Net I/σ(I): 8.79 |
Reflection shell | Resolution: 1.9→1.968 Å / Num. unique obs: 8042 / CC1/2: 0.335 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IDQ Resolution: 1.9→47.43 Å / SU ML: 0.2296 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2164 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→47.43 Å
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Refine LS restraints |
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LS refinement shell |
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