+Open data
-Basic information
Entry | Database: PDB / ID: 7npf | |||||||||
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Title | Vibrio cholerae ParA2-ATPyS-DNA filament | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / ATPase / Chromosome segregation / Bacterial cell division / filament | |||||||||
Function / homology | : / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / Chromosome partitioning protein ParA Function and homology information | |||||||||
Biological species | Vibrio cholerae (bacteria) Neoarius leptaspis (salmon catfish) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Parker, A.V. / Bergeron, J.R.C. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: The structure of the bacterial DNA segregation ATPase filament reveals the conformational plasticity of ParA upon DNA binding. Authors: Alexandra V Parker / Daniel Mann / Svetomir B Tzokov / Ling C Hwang / Julien R C Bergeron / Abstract: The efficient segregation of replicated genetic material is an essential step for cell division. Bacterial cells use several evolutionarily-distinct genome segregation systems, the most common of ...The efficient segregation of replicated genetic material is an essential step for cell division. Bacterial cells use several evolutionarily-distinct genome segregation systems, the most common of which is the type I Par system. It consists of an adapter protein, ParB, that binds to the DNA cargo via interaction with the parS DNA sequence; and an ATPase, ParA, that binds nonspecific DNA and mediates cargo transport. However, the molecular details of how this system functions are not well understood. Here, we report the cryo-EM structure of the Vibrio cholerae ParA2 filament bound to DNA, as well as the crystal structures of this protein in various nucleotide states. These structures show that ParA forms a left-handed filament on DNA, stabilized by nucleotide binding, and that ParA undergoes profound structural rearrangements upon DNA binding and filament assembly. Collectively, our data suggest the structural basis for ParA's cooperative binding to DNA and the formation of high ParA density regions on the nucleoid. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7npf.cif.gz | 584.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7npf.ent.gz | 491.6 KB | Display | PDB format |
PDBx/mmJSON format | 7npf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7npf_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7npf_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7npf_validation.xml.gz | 98.1 KB | Display | |
Data in CIF | 7npf_validation.cif.gz | 141.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/7npf ftp://data.pdbj.org/pub/pdb/validation_reports/np/7npf | HTTPS FTP |
-Related structure data
Related structure data | 12515MC 7npdC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 46440.969 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) Gene: parA, BC353_10845, C9J66_03480, D6U24_01990, ERS013138_01197, ERS013166_00021, ERS013186_00500, ERS013193_00027, ERS013198_00323, ERS013199_01186, ERS013200_00295, ERS013202_00851, ERS013206_ ...Gene: parA, BC353_10845, C9J66_03480, D6U24_01990, ERS013138_01197, ERS013166_00021, ERS013186_00500, ERS013193_00027, ERS013198_00323, ERS013199_01186, ERS013200_00295, ERS013202_00851, ERS013206_01885, EYB64_07940, F0315_18570, FLM02_03395, FXF03_20770, HPY05_13545 Production host: Escherichia coli (E. coli) / References: UniProt: A0A085S0Z4 #2: DNA chain | | Mass: 15302.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neoarius leptaspis (salmon catfish) #3: DNA chain | | Mass: 14860.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neoarius leptaspis (salmon catfish) #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-AGS / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: ParA2-ATPgS-DNA / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 52.02 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: -80.57 ° / Axial rise/subunit: 28.68 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182997 / Symmetry type: HELICAL |
Atomic model building | Protocol: OTHER |