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- PDB-6u9e: Structure of PdpA-VgrG Complex, Lidless -

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Basic information

Entry
Database: PDB / ID: 6u9e
TitleStructure of PdpA-VgrG Complex, Lidless
Components
  • PdpA
  • VgrG
KeywordsTRANSPORT PROTEIN / T6SS Central Spike / Complex
Function / homologyUncharacterized protein / PdpA
Function and homology information
Biological speciesFrancisella novicida (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.21 Å
AuthorsYang, X. / Clemens, D.L. / Lee, B.-Y. / Cui, Y. / Zhou, Z.H. / Horwitz, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorAI125497 United States
CitationJournal: Structure / Year: 2019
Title: Atomic Structure of the Francisella T6SS Central Spike Reveals a Unique α-Helical Lid and a Putative Cargo.
Authors: Xue Yang / Daniel L Clemens / Bai-Yu Lee / Yanxiang Cui / Z Hong Zhou / Marcus A Horwitz /
Abstract: Francisella bacteria rely on a phylogenetically distinct type VI secretion system (T6SS) to escape host phagosomes and cause the fatal disease tularemia, but the structural and molecular mechanisms ...Francisella bacteria rely on a phylogenetically distinct type VI secretion system (T6SS) to escape host phagosomes and cause the fatal disease tularemia, but the structural and molecular mechanisms involved are unknown. Here we report the atomic structure of the Francisella T6SS central spike complex, obtained by cryo-electron microscopy. Our structural and functional studies demonstrate that, unlike the single-protein spike composition of other T6SS subtypes, Francisella T6SS's central spike is formed by two proteins, PdpA and VgrG, akin to T4-bacteriophage gp27 and gp5, respectively, and that PdpA has unique characteristics, including a putative cargo within its cavity and an N-terminal helical lid. Structure-guided mutagenesis demonstrates that the PdpA N-terminal lid and C-terminal spike are essential to Francisella T6SS function. PdpA is thus both an adaptor, connecting VgrG to the tube, and a likely carrier of secreted cargo. These findings are important to understanding Francisella pathogenicity and designing therapeutics to combat tularemia.
History
DepositionSep 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: PdpA
C: PdpA
E: PdpA
B: VgrG
D: VgrG
F: VgrG


Theoretical massNumber of molelcules
Total (without water)348,0296
Polymers348,0296
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area42300 Å2
ΔGint-211 kcal/mol
Surface area100810 Å2

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Components

#1: Protein PdpA


Mass: 95469.961 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella novicida (bacteria) / Gene: pdpA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7X3I9
#2: Protein VgrG


Mass: 20539.779 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella novicida (bacteria) / Gene: B4919_03525 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7X3I8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PdpA-VgrG complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Francisella novicida (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 47 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16889 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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