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- PDB-2w6d: BACTERIAL DYNAMIN-LIKE PROTEIN LIPID TUBE BOUND -

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Basic information

Entry
Database: PDB / ID: 2w6d
TitleBACTERIAL DYNAMIN-LIKE PROTEIN LIPID TUBE BOUND
ComponentsDYNAMIN FAMILY PROTEIN
KeywordsHYDROLASE / 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
: / Bacterial dynamin-like protein, helical domain / Mitofusin family / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-CPL / GUANOSINE-5'-DIPHOSPHATE / Bacterial dynamin-like protein
Similarity search - Component
Biological speciesNOSTOC PUNCTIFORME (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 9 Å
AuthorsLow, H.H. / Sachse, C. / Amos, L.A. / Lowe, J.
CitationJournal: 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
DepositionDec 18, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Author supporting evidence / Data collection / Other / Category: cell / em_image_scans / em_single_particle_entity / Item: _cell.Z_PDB
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Assembly

Deposited unit
A: DYNAMIN FAMILY PROTEIN
B: DYNAMIN FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,67748
Polymers157,4362
Non-polymers34,24146
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein DYNAMIN FAMILY PROTEIN / BACTERIAL DYNAMIN-LIKE PROTEIN BDLP


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 / 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE


Mass: 758.060 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C42H80NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: BACTERIAL DYNAMIN-LIKE PROTEIN BDLP LIPID TUBE / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X
Image recordingFilm or detector model: GENERIC FILM
Radiation wavelengthRelative weight: 1

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Processing

3D reconstructionResolution: 9 Å / Resolution method: FSC 0.5 CUT-OFF / Details: NO REFINEMENT PERFORMED, MANUAL FITTING / Symmetry type: HELICAL
RefinementHighest resolution: 9 Å
Refinement stepCycle: LAST / Highest resolution: 9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10858 0 2344 0 13202

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