+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5129 | |||||||||
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Title | Reconstruction of ParM in the open state using cryo-EM | |||||||||
Map data | Reconstruction of ParM in the open state | |||||||||
Sample |
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Keywords | polymorphic protein polymers | |||||||||
Function / homology | Plasmid 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 species | unidentified (others) | |||||||||
Method | helical reconstruction / cryo EM | |||||||||
Authors | Galkin VE / Orlova A / Rivera C / Mullins RD / Egelman EH | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5129.map.gz | 822.8 KB | EMDB map data format | |
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Header (meta data) | emd-5129-v30.xml emd-5129.xml | 6.9 KB 6.9 KB | Display Display | EMDB header |
Images | emd_5129_1.jpg | 26.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5129 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5129 | HTTPS FTP |
-Validation report
Summary document | emd_5129_validation.pdf.gz | 269.7 KB | Display | EMDB validaton report |
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Full document | emd_5129_full_validation.pdf.gz | 269.2 KB | Display | |
Data in XML | emd_5129_validation.xml.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5129 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5129 | HTTPS FTP |
-Related structure data
Related structure data | 3ikyMC 5128C 3ikuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5129.map.gz / Format: CCP4 / Size: 7.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of ParM in the open state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ParM
Entire | Name: ParM |
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Components |
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-Supramolecule #1000: ParM
Supramolecule | Name: ParM / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: ParM
Macromolecule | Name: ParM / type: protein_or_peptide / ID: 1 / Name.synonym: ParM / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: unidentified (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: 626 / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 24.2 Å Applied symmetry - Helical parameters - Δ&Phi: 165 ° |
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