+Open data
-Basic information
Entry | Database: PDB / ID: 5d3q | ||||||
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Title | Dynamin 1 GTPase-BSE fusion dimer complexed with GDP | ||||||
Components | Dynamin-1,Dynamin-1 | ||||||
Keywords | HYDROLASE / Fusion protein / GTPase / Endocytosis | ||||||
Function / homology | Function and homology information clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / Formation of annular gap junctions ...clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / Formation of annular gap junctions / endosome organization / Gap junction degradation / photoreceptor ribbon synapse / membrane coat / Recycling pathway of L1 / phosphatidylinositol-3,4,5-trisphosphate binding / endocytic vesicle / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / photoreceptor inner segment / receptor-mediated endocytosis / cell projection / modulation of chemical synaptic transmission / protein homooligomerization / receptor internalization / endocytosis / : / GDP binding / presynapse / Clathrin-mediated endocytosis / microtubule binding / protein homotetramerization / microtubule / GTPase activity / glutamatergic synapse / synapse / GTP binding / protein kinase binding / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Anand, R. / Eschenburg, S. / Reubold, T.F. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2016 Title: Crystal structure of the GTPase domain and the bundle signalling element of dynamin in the GDP state. Authors: Anand, R. / Eschenburg, S. / Reubold, T.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d3q.cif.gz | 158 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d3q.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 5d3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d3q_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5d3q_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5d3q_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 5d3q_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/5d3q ftp://data.pdbj.org/pub/pdb/validation_reports/d3/5d3q | HTTPS FTP |
-Related structure data
Related structure data | 2x2eS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38527.035 Da / Num. of mol.: 2 Fragment: UNP residues 5-320, 726-746,UNP residues 5-320, 726-746 Source method: isolated from a genetically manipulated source Details: The sequence contains residues 5-320 and 726-746 of human dynamin 1. The very N-terminus contains a glycine residue from the TEV cleavage step. The two dynamin fragments are connected by a ...Details: The sequence contains residues 5-320 and 726-746 of human dynamin 1. The very N-terminus contains a glycine residue from the TEV cleavage step. The two dynamin fragments are connected by a linker sequence of eight residues (KHGTDSRV). Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1, DNM / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q05193, dynamin GTPase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Before crystallization set-ups, GG1 at a concentration of 10 mg/ml was supplemented with 2 mM GDP and 2 mM MgCl2 and incubated for 1 h on ice. GG1GDP was crystallized by hanging drop vapour ...Details: Before crystallization set-ups, GG1 at a concentration of 10 mg/ml was supplemented with 2 mM GDP and 2 mM MgCl2 and incubated for 1 h on ice. GG1GDP was crystallized by hanging drop vapour diffusion mixing 1.5 ul protein solution with 1.5 ul reservoir solution containing 0.1 M Tris (pH 8.0), 26 % PEG 3350 and 0.2 M NaSCN. The drops were equilibrated against 700 ul of reservoir. PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.626 Å / Num. obs: 72213 / % possible obs: 97.6 % / Redundancy: 4.63 % / Rmerge(I) obs: 0.118 / Rsym value: 0.108 / Net I/σ(I): 10.75 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 6.7 / % possible all: 96.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2x2e Resolution: 1.7→47.626 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.7 / 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: 1.7→47.626 Å
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Refine LS restraints |
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LS refinement shell |
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