2W6D

BACTERIAL DYNAMIN-LIKE PROTEIN LIPID TUBE BOUND


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. h.low@mail.cryst.bbk.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DYNAMIN FAMILY PROTEINA, B695Nostoc punctiforme PCC 73102Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2IZD3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPL
Query on CPL

Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
C [auth A],
CA [auth A],
DA [auth B],
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
 Ligand Interaction
GDP
Query on GDP

Download Ideal Coordinates CCD File 
D [auth A],
NA [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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