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- PDB-2qu4: Model for Bacterial ParM Filament -

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Basic information

Entry
Database: PDB / ID: 2qu4
TitleModel for Bacterial ParM Filament
ComponentsPlasmid segregation protein parM
KeywordsSTRUCTURAL PROTEIN / filament model / actin-like protein / helical polymer / 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: 16 Å
AuthorsOrlova, A. / Garner, E.C. / Galkin, V.E. / Heuser, J. / Mullins, R.D. / Egelman, E.H.
CitationJournal: Nat Struct Mol Biol / Year: 2007
Title: The structure of bacterial ParM filaments.
Authors: Albina Orlova / Ethan C Garner / Vitold E Galkin / John Heuser / R Dyche Mullins / Edward H Egelman /
Abstract: Bacterial ParM is a homolog of eukaryotic actin and is involved in moving plasmids so that they segregate properly during cell division. Using cryo-EM and three-dimensional reconstruction, we show ...Bacterial ParM is a homolog of eukaryotic actin and is involved in moving plasmids so that they segregate properly during cell division. Using cryo-EM and three-dimensional reconstruction, we show that ParM filaments have a different structure from F-actin, with very different subunit-subunit interfaces. These interfaces result in the helical handedness of the ParM filament being opposite to that of F-actin. Like F-actin, ParM filaments have a variable twist, and we show that this involves domain-domain rotations within the ParM subunit. The present results yield new insights into polymorphisms within F-actin, as well as the evolution of polymer families.
History
DepositionAug 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_single_particle_entity / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as representative helical assembly
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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Plasmid segregation protein parM


Theoretical massNumber of molelcules
Total (without water)35,8041
Polymers35,8041
Non-polymers00
Water0
1
A: Plasmid segregation protein parM
x 10


Theoretical massNumber of molelcules
Total (without water)358,04410
Polymers358,04410
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation9
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 10 / Rise per n subunits: 25 Å / Rotation per n subunits: 165.43 °)

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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.: 1 / Source method: isolated from a natural source / Source: (natural) 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: Plasmid segregation protein parM / Type: COMPLEX / Details: Helical
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm
Image recordingFilm or detector model: GENERIC FILM
Image scansScanner model: NIKON COOLSCAN

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Processing

3D reconstructionMethod: IHRSR / Resolution: 16 Å / Num. of particles: 3351 / Nominal pixel size: 2.4 Å / Actual pixel size: 2.4 Å / Magnification calibration: TMV / Symmetry type: HELICAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11MWM

1mwm

11MWM1PDBexperimental model
21MWK

1mwk

11MWK2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 0 0 2517

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