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

Open data

ID or keywords:


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Basic information

Database: EMDB / ID: 5129
TitleReconstruction of ParM in the open state using cryo-EM
Map dataReconstruction of ParM in the open state
Keywordspolymorphic protein polymers
Function / homologyPlasmid segregation protein ParM/StbA / StbA protein / plasmid partitioning / identical protein binding / Plasmid segregation protein ParM
Function and homology information
Sourceunidentified (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
Validation ReportPDB-ID: 3iky

SummaryFull reportAbout validation report
DateDeposition: Aug 6, 2009 / Header (metadata) release: Aug 24, 2009 / Map release: Sep 17, 2009 / Last update: Apr 2, 2014

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 2000
  • Imaged by UCSF Chimera
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  • 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:
Supplemental images

Downloads & links


Fileemd_5129.map.gz (map file in CCP4 format, 7814 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
2.38 Å/pix.
= 476. Å
100 pix
2.38 Å/pix.
= 238. Å
100 pix
2.38 Å/pix.
= 238. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.38 Å
Contour Level:1000 (by author), 2000 (movie #1):
Minimum - Maximum-974.88922119 - 6558.34570313
Average (Standard dev.)112.41428375 (600.58074951)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 238.00002 Å / B: 238.00002 Å / C: 476.00003 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ-34-26-72
MAP C/R/S123
start NC/NR/NS-50-50-100
D min/max/mean-974.8896558.346112.414

Supplemental data

Sample components

Entire ParM

EntireName: ParM / Number of components: 1

Component #1: protein, ParM

ProteinName: ParM / a.k.a: ParM / Recombinant expression: No
SourceSpecies: unidentified (others)

Experimental details

Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersHand: RIGHT HANDED / Delta z: 24.2 Å / Delta phi: 165 deg.
VitrificationInstrument: NONE / Cryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: 626 / Model: GATAN LIQUID NITROGEN

Image processing

ProcessingMethod: helical reconstruction

Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 1MWK
Output model

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