+Open data
-Basic information
Entry | Database: PDB / ID: 6bqw | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | AlfA Filament bound to AMPPNP | ||||||||||||
Components | Bacterial actin AlfA | ||||||||||||
Keywords | CYTOSOLIC PROTEIN / actin / plasmid segregation / filament | ||||||||||||
Function / homology | Actin-like protein, N-terminal / Actin like proteins N terminal domain / ATPase, nucleotide binding domain / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Actin-like protein N-terminal domain-containing protein Function and homology information | ||||||||||||
Biological species | Bacillus subtilis (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||
Authors | Usluer, G.D. / Kollman, J.M. / DiMaio, F. | ||||||||||||
Funding support | United States, Canada, Turkey, 3items
| ||||||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Cryo-EM structure of the bacterial actin AlfA reveals unique assembly and ATP-binding interactions and the absence of a conserved subdomain. Authors: Gülsima D Usluer / Frank DiMaio / Shun Kai Yang / Jesse M Hansen / Jessica K Polka / R Dyche Mullins / Justin M Kollman / Abstract: Bacterial actins are an evolutionarily diverse family of ATP-dependent filaments built from protomers with a conserved structural fold. Actin-based segregation systems are encoded on many bacterial ...Bacterial actins are an evolutionarily diverse family of ATP-dependent filaments built from protomers with a conserved structural fold. Actin-based segregation systems are encoded on many bacterial plasmids and function to partition plasmids into daughter cells. The bacterial actin AlfA segregates plasmids by a mechanism distinct from other partition systems, dependent on its unique dynamic properties. Here, we report the near-atomic resolution electron cryo-microscopy structure of the AlfA filament, which reveals a strikingly divergent filament architecture resulting from the loss of a subdomain conserved in all other actins and a mode of ATP binding. Its unusual assembly interfaces and nucleotide interactions provide insight into AlfA dynamics, and expand the range of evolutionary variation accessible to actin quaternary structure. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6bqw.cif.gz | 421.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6bqw.ent.gz | 340 KB | Display | PDB format |
PDBx/mmJSON format | 6bqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bqw_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6bqw_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6bqw_validation.xml.gz | 79.9 KB | Display | |
Data in CIF | 6bqw_validation.cif.gz | 99.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/6bqw ftp://data.pdbj.org/pub/pdb/validation_reports/bq/6bqw | HTTPS FTP |
-Related structure data
Related structure data | 7134MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 31150.414 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O52947 #2: Chemical | ChemComp-ANP / |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: AlfA filament / Type: COMPLEX Details: Each protomer is bound to the non-hydrolyzable nucleotide analog AMPPNP Entity ID: #1 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 12750 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Bacillus subtilis (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Filaments were assembled in 5 mM AMPPNP for 15 minutes at room temperature |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 72 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Helical symmerty | Angular rotation/subunit: 157.7 ° / Axial rise/subunit: 24.4 Å / Axial symmetry: C1 | ||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113222 / Symmetry type: HELICAL | ||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |