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- EMDB-5129: Reconstruction of ParM in the open state using cryo-EM -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-5129
TitleReconstruction of ParM in the open state using cryo-EM
Map dataReconstruction of ParM in the open state
Sample
  • Sample: ParM
  • Protein or peptide: ParM
Keywordspolymorphic protein polymers
Function / homologyPlasmid segregation protein ParM/StbA / : / : / Plasmid segregation protein ParM, N-terminal / Plasmid segregation protein ParM, C-terminal / plasmid partitioning / ATPase, nucleotide binding domain / identical protein binding / Plasmid segregation protein ParM
Function and homology information
Biological speciesunidentified (others)
Methodhelical reconstruction / cryo EM
AuthorsGalkin VE / Orlova A / Rivera C / Mullins RD / Egelman EH
CitationJournal: Structure / Year: 2009
Title: Structural polymorphism of the ParM filament and dynamic instability.
Authors: Vitold E Galkin / Albina Orlova / Chris Rivera / R Dyche Mullins / Edward H Egelman /
Abstract: Segregation of the R1 plasmid in bacteria relies on ParM, an actin homolog that segregates plasmids by switching between cycles of polymerization and depolymerization. We find similar polymerization ...Segregation of the R1 plasmid in bacteria relies on ParM, an actin homolog that segregates plasmids by switching between cycles of polymerization and depolymerization. We find similar polymerization kinetics and stability in the presence of either ATP or GTP and a 10-fold affinity preference for ATP over GTP. We used electron cryo-microscopy to evaluate the heterogeneity within ParM filaments. In addition to variable twist, ParM has variable axial rise, and both parameters are coupled. Subunits in the same ParM filaments can exist in two different structural states, with the nucleotide-binding cleft closed or open, and the bound nucleotide biases the distribution of states. The interface between protomers is different between these states, and in neither state is it similar to F-actin. Our results suggest that the closed state of the cleft is required but not sufficient for ParM polymerization, and provide a structural basis for the dynamic instability of ParM filaments.
History
DepositionAug 6, 2009-
Header (metadata) releaseAug 24, 2009-
Map releaseSep 17, 2009-
UpdateApr 2, 2014-
Current statusApr 2, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2000
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3iky
  • Surface level: 2000
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5129_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5129.map.gz / Format: CCP4 / Size: 7.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of ParM in the open state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.38 Å/pix.
x 200 pix.
= 476. Å		2.38 Å/pix.
x 100 pix.
= 238. Å		2.38 Å/pix.
x 100 pix.
= 238. 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: 2.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1000.0 / Movie #1: 2000
Minimum - Maximum-974.889221189999944 - 6558.345703130000402
Average (Standard dev.)112.414283749999996 (±600.580749510000032)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-100
Dimensions100100200
Spacing100100200
CellA: 238.00002 Å / B: 238.00002 Å / C: 476.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.382.382.38
M x/y/z100100200
origin x/y/z0.0000.0000.000
length x/y/z238.000238.000476.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-50-50-100
NC/NR/NS100100200
D min/max/mean-974.8896558.346112.414

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Supplemental data

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Sample components

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Entire : ParM

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

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Supramolecule #1000: ParM

SupramoleculeName: ParM / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: ParM

MacromoleculeName: ParM / type: protein_or_peptide / ID: 1 / Name.synonym: ParM / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others)

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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 TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: 626 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 24.2 Å
Applied symmetry - Helical parameters - Δ&Phi: 165 °

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Atomic model buiding 1

Initial modelPDB ID:

1mwk

RefinementSpace: REAL
Output model

PDB-3iky:
Structural model of ParM filament in the open state by cryo-EM

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