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- EMDB-1589: Bacterial dynamin-like protein undergoes radical conformational c... -

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Basic information

Entry
Database: EMDB / ID: EMD-1589
TitleBacterial dynamin-like protein undergoes radical conformational changes that promote membrane curvature
Map dataBacterial dynamin BDLP lipid tube reconstruction, single-particle cryo EM helical reconstruction
Sample
  • Sample: Bacterial dynamin-like protein BDLP
  • Protein or peptide: Bacterial dynamin-like protein BDLP
Keywordsdynamin / membrane / GTPase
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
Bacterial dynamin-like protein
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsLow HH / Sachse C / Amos LA / 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, 2008-
Header (metadata) releaseJan 6, 2009-
Map releaseJan 22, 2010-
UpdateApr 9, 2014-
Current statusApr 9, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.47
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.47
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2w6d
  • Surface level: 1.47
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2w6d
  • Surface level: 1.47
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2w6d
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1589.png

Downloads & links

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Map

FileDownload / File: emd_1589.map.gz / Format: CCP4 / Size: 32.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacterial dynamin BDLP lipid tube reconstruction, single-particle cryo EM helical reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
2.03 Å/pix.
x 81 pix.
= 671.213 Å		2.03 Å/pix.
x 330 pix.
= 671.213 Å		2.03 Å/pix.
x 330 pix.
= 671.213 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2.03398 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 1.47 / Movie #1: 1.47
Minimum - Maximum-3.49485 - 4.64403
Average (Standard dev.)0.00625484 (±1.00075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-165-165-40
Dimensions33033081
Spacing33033081
CellA=B=C: 671.213 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.03397878787882.03397878787882.0339787878788
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z671.213671.213671.213
α/β/γ90.00090.00090.000
start NX/NY/NZ-165-165-40
NX/NY/NZ33033081
MAP C/R/S213
start NC/NR/NS-165-165-40
NC/NR/NS33033081
D min/max/mean-3.4954.6440.006

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Supplemental data

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Sample components

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Entire : Bacterial dynamin-like protein BDLP

EntireName: Bacterial dynamin-like protein BDLP
Components
  • Sample: Bacterial dynamin-like protein BDLP
  • Protein or peptide: Bacterial dynamin-like protein BDLP

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Supramolecule #1000: Bacterial dynamin-like protein BDLP

SupramoleculeName: Bacterial dynamin-like protein BDLP / type: sample / ID: 1000
Oligomeric state: BDLP dimer is the asymmetric unit of the tubes
Number unique components: 1

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Macromolecule #1: Bacterial dynamin-like protein BDLP

MacromoleculeName: Bacterial dynamin-like protein BDLP / type: protein_or_peptide / ID: 1 / Name.synonym: BDLP / Oligomeric state: dimer / Recombinant expression: Yes
Source (natural)Organism: Nostoc punctiforme (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingCategory: FILM / Film or detector model: GENERIC FILM / Digitization - Scanner: OTHER
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 59000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 3.1926 Å
Applied symmetry - Helical parameters - Δ&Phi: 63.815 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
CTF correctionDetails: CTF2, CTFTILT

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Atomic model buiding 1

Initial modelPDB ID:

2j68


Chain - Chain ID: A
DetailsPDBEntryID_givenInChain. Protocol: manual. very large conformational changes.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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