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- PDB-2zhc: ParM filament -

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Basic information

Entry
Database: PDB / ID: 2zhc
TitleParM filament
ComponentsPlasmid segregation protein parM
KeywordsCELL CYCLE/PROTEIN FIBRIL / ParM / Plasmid / Plasmid partition / CELL CYCLE-PROTEIN FIBRIL COMPLEX
Function / homology
Function and homology information


plasmid partitioning / identical protein binding
Similarity search - Function
Plasmid segregation protein ParM/StbA / : / Plasmid segregation protein ParM, N-terminal / Plasmid segregation protein ParM, C-terminal / ParM-like / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Plasmid segregation protein ParM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / negative staining / Resolution: 23 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 4, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Data collection / Database references
Category: database_2 / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_vitrification / pdbx_initial_refinement_model / refine / struct_conn / struct_site
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 / _refine.ls_d_res_high / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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Assembly

Deposited unit
A: Plasmid segregation protein parM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2563
Polymers35,8041
Non-polymers4522
Water00
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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: parM, stbA / Plasmid: PMD137 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P11904
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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 / Type: COMPLEX / Details: stained with 1.0 % uranyl acetate
Buffer solutionName: 10mM Hepes, 25mM KCl, 1mM MgCl2, 1mM DTT, 5mM GMPPNP / pH: 7.5
Details: 10mM Hepes, 25mM KCl, 1mM MgCl2, 1mM DTT, 5mM GMPPNP
SpecimenConc.: 0.13 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl Acetate
Specimen supportDetails: Carbon

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Electron microscopy imaging

MicroscopyModel: JEOL 2010HC / Date: Jan 1, 2007
Electron gunElectron source: LAB6 / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Nominal defocus max: 10300 nm / Nominal defocus min: 3700 nm
Specimen holderTemperature: 300 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 12 e/Å2 / Film or detector model: GENERIC FILM
Image scansNum. digital images: 2085
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: EOS / Category: 3D reconstruction
CTF correctionDetails: Phase and Amplitude
3D reconstructionMethod: Single particle analysis / Resolution: 23 Å / Num. of particles: 2085 / Nominal pixel size: 4.011 Å / Actual pixel size: 4.011 Å
Details: This data was achieved by negative staining experiments
Symmetry type: HELICAL
Atomic model buildingPDB-ID: 1MWM

1mwm


Accession code: 1MWM / Source name: PDB / Type: experimental model
RefinementHighest resolution: 23 Å
Details: This data was achieved by negative staining experiments
Refinement stepCycle: LAST / Highest resolution: 23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 40 0 5067

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