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

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Basic information

Entry
Database: PDB / ID: 3iky
TitleStructural model of ParM filament in the open state by cryo-EM
ComponentsPlasmid segregation protein parM
KeywordsSTRUCTURAL PROTEIN / polymorphic protein polymers / Plasmid / Plasmid partition
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 18 Å
AuthorsGalkin, V.E. / Orlova, A. / Rivera, C. / Mullins, R.D. / Egelman, E.H.
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, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / em_single_particle_entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Plasmid segregation protein parM
B: Plasmid segregation protein parM
C: Plasmid segregation protein parM
D: Plasmid segregation protein parM
E: Plasmid segregation protein parM
F: Plasmid segregation protein parM
G: Plasmid segregation protein parM
H: Plasmid segregation protein parM
I: Plasmid segregation protein parM
J: Plasmid segregation protein parM
K: Plasmid segregation protein parM
L: Plasmid segregation protein parM


Theoretical massNumber of molelcules
Total (without water)429,65312
Polymers429,65312
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Plasmid segregation protein parM / Protein stbA / ParA locus 36 kDa protein


Mass: 35804.375 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: parM, stbA / Production host: Escherichia coli (E. coli) / References: UniProt: P11904

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: ParM Filament in Open State / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

3D reconstructionMethod: IHRSR / Resolution: 18 Å / Nominal pixel size: 2.38 Å / Actual pixel size: 2.38 Å / Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms30192 0 0 0 30192

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