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- EMDB-1470: Molecular structure of the ParM polymer and the mechanism leading... -

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Basic information

Entry
Database: EMDB / ID: EMD-1470
TitleMolecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability
Map dataA volume file of ParM filament
Sample
  • Sample: ParM filament
  • Protein or peptide: ParM
KeywordsGTPase / molecular switch / filament / ParM
Function / homologyPlasmid segregation protein ParM/StbA / : / Plasmid segregation protein ParM, N-terminal / Plasmid segregation protein ParM, C-terminal / ParM-like / plasmid partitioning / ATPase, nucleotide binding domain / identical protein binding / Plasmid segregation protein ParM
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / negative staining / Resolution: 23.0 Å
AuthorsPopp D / Narita A / Oda T / Fujisawa T / Matsuo H / Nitanai Y / Iwasa M / Maeda K / Onishi H / Maeda Y
CitationJournal: EMBO J / Year: 2008
Title: Molecular structure of the ParM polymer and the mechanism leading to its nucleotide-driven dynamic instability.
Authors: David Popp / Akihiro Narita / Toshiro Oda / Tetsuro Fujisawa / Hiroshi Matsuo / Yasushi Nitanai / Mitsusada Iwasa / Kayo Maeda / Hirofumi Onishi / Yuichiro Maéda /
Abstract: ParM is a prokaryotic actin homologue, which ensures even plasmid segregation before bacterial cell division. In vivo, ParM forms a labile filament bundle that is reminiscent of the more complex ...ParM is a prokaryotic actin homologue, which ensures even plasmid segregation before bacterial cell division. In vivo, ParM forms a labile filament bundle that is reminiscent of the more complex spindle formed by microtubules partitioning chromosomes in eukaryotic cells. However, little is known about the underlying structural mechanism of DNA segregation by ParM filaments and the accompanying dynamic instability. Our biochemical, TIRF microscopy and high-pressure SAX observations indicate that polymerization and disintegration of ParM filaments is driven by GTP rather than ATP and that ParM acts as a GTP-driven molecular switch similar to a G protein. Image analysis of electron micrographs reveals that the ParM filament is a left-handed helix, opposed to the right-handed actin polymer. Nevertheless, the intersubunit contacts are similar to those of actin. Our atomic model of the ParM-GMPPNP filament, which also fits well to X-ray fibre diffraction patterns from oriented gels, can explain why after nucleotide release, large conformational changes of the protomer lead to a breakage of intra- and interstrand interactions, and thus to the observed disintegration of the ParM filament after DNA segregation.
History
DepositionFeb 14, 2008-
Header (metadata) releaseFeb 19, 2008-
Map releaseMar 31, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9.0672E-5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 9.0672E-5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1470.gif

Downloads & links

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Map

FileDownload / File: emd_1470.map.gz / Format: CCP4 / Size: 257.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA volume file of ParM filament
Voxel sizeX=Y=Z: 4.011 Å
Density
Contour Level1: 0.00012 / Movie #1: 9.07E-5
Minimum - Maximum-0.0000698964 - 0.000182333
Average (Standard dev.)0.00000682298 (±0.000045134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions404042
Spacing404042
CellA: 160.44 Å / B: 160.44 Å / C: 168.462 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.0114.0114.011
M x/y/z404042
origin x/y/z0.0000.0000.000
length x/y/z160.440160.440168.462
α/β/γ90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS404042
D min/max/mean-0.0000.0000.000

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Supplemental data

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Sample components

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Entire : ParM filament

EntireName: ParM filament
Components
  • Sample: ParM filament
  • Protein or peptide: ParM

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Supramolecule #1000: ParM filament

SupramoleculeName: ParM filament / type: sample / ID: 1000 / Oligomeric state: Filament / Number unique components: 1
Molecular weightTheoretical: 35 KDa

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Macromolecule #1: ParM

MacromoleculeName: ParM / type: protein_or_peptide / ID: 1 / Name.synonym: ParM / Number of copies: 10 / Oligomeric state: Helical filament / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.14 mg/mL
BufferpH: 7.5
Details: 10 mM Hepes, 25 mM KCl, 1 mM MgCl2, 1 mM DTT, 5 mM GMPPNP
StainingType: NEGATIVE / Details: 1.0 % uranyl acetate
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2010HC
Electron beamAcceleration voltage: 100 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: OTHER
Image recordingDigitization - Sampling interval: 7 µm / Number real images: 7

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Image processing

CTF correctionDetails: Each filament
Final reconstructionResolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EOS

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Atomic model buiding 1

Initial modelPDB ID:

1mwm


Chain - Chain ID: A
SoftwareName: situs
DetailsPDBEntryID_givenInChain. Protocol: Rigid body. After rigid body fitting the structure was refined by energy minimization with program NAMD
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2zhc:
ParM filament

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