+Open data
-Basic information
Entry | Database: PDB / ID: 2w6d | ||||||
---|---|---|---|---|---|---|---|
Title | BACTERIAL DYNAMIN-LIKE PROTEIN LIPID TUBE BOUND | ||||||
Components | DYNAMIN FAMILY PROTEIN | ||||||
Keywords | HYDROLASE / GTPASE / DYNAMIN / MITOFUSIN / TUBULATION / MEMEBRANE DYNAMICS | ||||||
Function / homology | Function and homology information dynamin GTPase / mitochondrial fusion / GTPase activity / lipid binding / GTP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | NOSTOC PUNCTIFORME (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 9 Å | ||||||
Authors | Low, H.H. / Sachse, C. / Amos, L.A. / Lowe, J. | ||||||
Citation | Journal: Cell / Year: 2009 Title: Structure of a bacterial dynamin-like protein lipid tube provides a mechanism for assembly and membrane curving. Authors: Harry H Low / Carsten Sachse / Linda A Amos / Jan Löwe / Abstract: Proteins of the dynamin superfamily mediate membrane fission, fusion, and restructuring events by polymerizing upon lipid bilayers and forcing regions of high curvature. In this work, we show the ...Proteins of the dynamin superfamily mediate membrane fission, fusion, and restructuring events by polymerizing upon lipid bilayers and forcing regions of high curvature. In this work, we show the electron cryomicroscopy reconstruction of a bacterial dynamin-like protein (BDLP) helical filament decorating a lipid tube at approximately 11 A resolution. We fitted the BDLP crystal structure and produced a molecular model for the entire filament. The BDLP GTPase domain dimerizes and forms the tube surface, the GTPase effector domain (GED) mediates self-assembly, and the paddle region contacts the lipids and promotes curvature. Association of BDLP with GMPPNP and lipid induces radical, large-scale conformational changes affecting polymerization. Nucleotide hydrolysis seems therefore to be coupled to polymer disassembly and dissociation from lipid, rather than membrane restructuring. Observed structural similarities with rat dynamin 1 suggest that our results have broad implication for other dynamin family members. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2w6d.cif.gz | 331.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2w6d.ent.gz | 278.3 KB | Display | PDB format |
PDBx/mmJSON format | 2w6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w6d_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2w6d_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 2w6d_validation.xml.gz | 79.5 KB | Display | |
Data in CIF | 2w6d_validation.cif.gz | 105.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/2w6d ftp://data.pdbj.org/pub/pdb/validation_reports/w6/2w6d | HTTPS FTP |
-Related structure data
Related structure data | 1589MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (1), |
-Components
#1: Protein | Mass: 78717.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NOSTOC PUNCTIFORME (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B2IZD3 #2: Chemical | ChemComp-CPL / #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: BACTERIAL DYNAMIN-LIKE PROTEIN BDLP LIPID TUBE / Type: COMPLEX |
---|---|
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Cryogen name: ETHANE / Details: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X |
Image recording | Film or detector model: GENERIC FILM |
Radiation wavelength | Relative weight: 1 |
-Processing
3D reconstruction | Resolution: 9 Å / Resolution method: FSC 0.5 CUT-OFF / Details: NO REFINEMENT PERFORMED, MANUAL FITTING / Symmetry type: HELICAL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Highest resolution: 9 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 9 Å
|