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- PDB-6h3j: Structural snapshots of the Type 9 protein translocon Plug-complex -

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Basic information

Entry
Database: PDB / ID: 6h3j
TitleStructural snapshots of the Type 9 protein translocon Plug-complex
Components
  • Peptidyl-prolyl cis-trans isomeraseProlyl isomerase
  • Plug
  • Protein involved in gliding motility SprA
KeywordsPROTEIN TRANSPORT / Type 9 Secretion System Type IX Secretion System T9S folded protein secretion outer membrane protein
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
Protein of unknown function DUF5103 / Type 9 secretion system plug protein 1st domain / Gliding motility protein SprA N-terminal domain / Cell surface SprA / Motility related/secretion protein / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Protein involved in gliding motility SprA / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / SprA
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDeme, J.C. / Lea, S.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust107929/Z/15/Z United Kingdom
Wellcome Trust100298 United Kingdom
CitationJournal: Nature / Year: 2018
Title: Type 9 secretion system structures reveal a new protein transport mechanism.
Authors: Frédéric Lauber / Justin C Deme / Susan M Lea / Ben C Berks /
Abstract: The type 9 secretion system (T9SS) is the protein export pathway of bacteria of the Gram-negative Fibrobacteres-Chlorobi-Bacteroidetes superphylum and is an essential determinant of pathogenicity in ...The type 9 secretion system (T9SS) is the protein export pathway of bacteria of the Gram-negative Fibrobacteres-Chlorobi-Bacteroidetes superphylum and is an essential determinant of pathogenicity in severe periodontal disease. The central element of the T9SS is a so-far uncharacterized protein-conducting translocon located in the bacterial outer membrane. Here, using cryo-electron microscopy, we provide structural evidence that the translocon is the T9SS protein SprA. SprA forms an extremely large (36-strand) single polypeptide transmembrane β-barrel. The barrel pore is capped on the extracellular end, but has a lateral opening to the external membrane surface. Structures of SprA bound to different components of the T9SS show that partner proteins control access to the lateral opening and to the periplasmic end of the pore. Our results identify a protein transporter with a distinctive architecture that uses an alternating access mechanism in which the two ends of the protein-conducting channel are open at different times.
History
DepositionJul 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Protein involved in gliding motility SprA
B: Peptidyl-prolyl cis-trans isomerase
C: Plug


Theoretical massNumber of molelcules
Total (without water)338,0743
Polymers338,0743
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-3 kcal/mol
Surface area100940 Å2
MethodPISA

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Components

#1: Protein Protein involved in gliding motility SprA


Mass: 270251.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5G5I4, UniProt: Q5I6C7*PLUS
#2: Protein Peptidyl-prolyl cis-trans isomerase / Prolyl isomerase


Mass: 19219.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101 / References: UniProt: A5F9W9, peptidylprolyl isomerase
#3: Protein Plug


Mass: 48602.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A5FJ36

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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: Complex of SprA, PPI and Plug / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.335 MDa / Experimental value: NO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 52 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1SIMPLE2particle selection
4SIMPLE2CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION2initial Euler assignment
11RELION2final Euler assignment
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1100000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150000 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL / Target criteria: Correlation

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