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- PDB-6bqw: AlfA Filament bound to AMPPNP -

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Database: PDB / ID: 6bqw
TitleAlfA Filament bound to AMPPNP
ComponentsBacterial actin AlfA
KeywordsCYTOSOLIC PROTEIN / actin / plasmid segregation / filament
Function / homologyActin-like protein, N-terminal / Actin like proteins N terminal domain / Uncharacterized protein
Function and homology information
Specimen sourceBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 4.2 Å resolution
AuthorsUsluer, G.D. / Kollman, J.M. / DiMaio, F.
CitationJournal: 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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 28, 2017 / Release: Feb 28, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 28, 2018Structure modelrepositoryInitial release
1.1Apr 11, 2018Structure modelData collection / Database references / Structure summarycitation / entity / struct_citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description / _struct.pdbx_descriptor

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Deposited unit
A: Bacterial actin AlfA
B: Bacterial actin AlfA
C: Bacterial actin AlfA
D: Bacterial actin AlfA
E: Bacterial actin AlfA
F: Bacterial actin AlfA
G: Bacterial actin AlfA
H: Bacterial actin AlfA
I: Bacterial actin AlfA
hetero molecules

Theoretical massNumber of molelcules
Total (without water)284,90918

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)25300
ΔGint (kcal/M)-102
Surface area (Å2)92870


#1: Protein/peptide
Bacterial actin AlfA / AlfA

Mass: 31150.414 Da / Num. of mol.: 9 / Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O52947
#2: Chemical

Mass: 506.196 Da / Num. of mol.: 9 / Formula: C10H17N6O12P3 / Comment: AMP-PNP (energy-carrying molecule analogue) *YM

Experimental details


EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

Sample preparation

ComponentName: AlfA filament / Type: COMPLEX
Details: Each protomer is bound to the non-hydrolyzable nucleotide analog AMPPNP
Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 12750 kDa/nm / Experimental value: NO
Source (natural)Organism: Bacillus subtilis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.16 mg/ml
Details: Filaments were assembled in 5 mM AMPPNP for 15 minutes at room temperature
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 72 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


EM software
2Leginonimage acquisition
12RELION2.03D reconstruction
13RosettaEMmodel refinement
Helical symmertyAngular rotation/subunit: 157.7 deg. / Axial rise/subunit: 24.4 Å / Axial symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 113222 / Symmetry type: HELICAL
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL

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