2W6D

BACTERIAL DYNAMIN-LIKE PROTEIN LIPID TUBE BOUND

• PDB DOI:  https://doi.org/10.2210/pdb2W6D/pdb
• EM Map EMD-1589: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Nostoc punctiforme PCC 73102
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-18 Released: 2009-12-22 
• Deposition Author(s): Low, H.H., Sachse, C., Amos, L.A., Lowe, J.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 9.00 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Structure of a Bacterial Dynamin-Like Protein Lipid Tube Provides a Mechanism for Assembly and Membrane Curving.

Low, H.H., Sachse, C., Amos, L.A., Lowe, J.

(2009) Cell 139: 1342-1352

• PubMed: 20064379 
• DOI: https://doi.org/10.1016/j.cell.2009.11.003
• Primary Citation of Related Structures:  
  2W6D


• PubMed 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 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.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 191.68 kDa 
• Atom Count: 13,202 
• Modelled Residue Count: 1,360 
• Deposited Residue Count: 1,390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DYNAMIN FAMILY PROTEIN	A, B	695	Nostoc punctiforme PCC 73102	Mutation(s): 0  Gene Names: Npun_R6513 EC: 3.6.5.5
UniProt
Find proteins for B2IZD3 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore B2IZD3  Go to UniProtKB:  B2IZD3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPL	AA [auth A], BA [auth A], C [auth A], CA [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], X [auth A], Y [auth A], Z [auth A]	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C42 H80 N O8 P JLPULHDHAOZNQI-ZTIMHPMXSA-N
GDP	D [auth A], NA [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 9.00 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Low, H.H., Sachse, C., Amos, L.A., Lowe, J.

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-10-23
  Changes: Author supporting evidence, Data collection, Other