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- PDB-5zdh: CryoEM structure of ETEC Pilotin-Secretin AspS-GspD complex -

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Basic information

Entry
Database: PDB / ID: 5zdh
TitleCryoEM structure of ETEC Pilotin-Secretin AspS-GspD complex
Components
  • Type II secretion system lipoproteinType II secretion system
  • Type II secretion system protein DType II secretion system
KeywordsPROTEIN TRANSPORT / Pilotin / Secretin
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane
Similarity search - Function
Type II secretion system (T2SS) pilotin, S protein / Type II secretion system (T2SS) pilotin, S protein / : / GspD-like, N0 domain / Ribosomal Protein S8; Chain: A, domain 1 - #120 / Type II secretion system protein GspD / GspD/PilQ family / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily ...Type II secretion system (T2SS) pilotin, S protein / Type II secretion system (T2SS) pilotin, S protein / : / GspD-like, N0 domain / Ribosomal Protein S8; Chain: A, domain 1 - #120 / Type II secretion system protein GspD / GspD/PilQ family / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein / Ribosomal Protein S8; Chain: A, domain 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Secretin GspD 2 / Pilotin AspS 2
Similarity search - Component
Biological speciesEscherichia coli O78:H11
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYin, M. / Yan, Z. / Li, X.
CitationJournal: Nat Microbiol / Year: 2018
Title: Structural insight into the assembly of the type II secretion system pilotin-secretin complex from enterotoxigenic Escherichia coli.
Authors: Meng Yin / Zhaofeng Yan / Xueming Li /
Abstract: Secretin is a large outer-membrane channel found in secretion systems of Gram-negative bacteria, facilitating the last step for transfer of proteins into the extracellular environment. In the type II ...Secretin is a large outer-membrane channel found in secretion systems of Gram-negative bacteria, facilitating the last step for transfer of proteins into the extracellular environment. In the type II secretion system, a lipoprotein called pilotin is essential to bind and target its corresponding secretin to the outer membrane. However, there is only limited structural information available about the interaction and assembly of the pilotin-secretin complex. Here we report the first near-atomic-resolution structure of a full-length Vibrio-type pilotin-secretin (AspS-GspD) complex from enterotoxigenic Escherichia coli by cryo-electron microscopy, which reveals the detailed assembly mode of the full-length pilotin-secretin complex. The AspS subunits attach to the secretin channel surface with a 15:15 stoichiometric ratio to GspD subunits, and insert their amino terminus into the outer membrane. The AspS subunits interact with all three secondary structural elements of the S domain of GspD, including strong interaction with the carboxy-terminal α-helix and weak interactions with another two elements, an α-helix and a loop. These structural and biochemical details provide a deeper insight to pilotin-secretin interaction and their assembly mode.
History
DepositionFeb 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Assembly

Deposited unit
A: Type II secretion system protein D
B: Type II secretion system protein D
C: Type II secretion system protein D
D: Type II secretion system protein D
E: Type II secretion system protein D
F: Type II secretion system protein D
G: Type II secretion system protein D
H: Type II secretion system protein D
I: Type II secretion system protein D
J: Type II secretion system protein D
K: Type II secretion system protein D
L: Type II secretion system protein D
M: Type II secretion system protein D
N: Type II secretion system protein D
O: Type II secretion system protein D
P: Type II secretion system lipoprotein
Q: Type II secretion system lipoprotein
R: Type II secretion system lipoprotein
S: Type II secretion system lipoprotein
T: Type II secretion system lipoprotein
U: Type II secretion system lipoprotein
V: Type II secretion system lipoprotein
W: Type II secretion system lipoprotein
X: Type II secretion system lipoprotein
Y: Type II secretion system lipoprotein
Z: Type II secretion system lipoprotein
a: Type II secretion system lipoprotein
b: Type II secretion system lipoprotein
c: Type II secretion system lipoprotein
d: Type II secretion system lipoprotein


Theoretical massNumber of molelcules
Total (without water)1,228,29930
Polymers1,228,29930
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area208830 Å2
ΔGint-1061 kcal/mol
Surface area374130 Å2

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Components

#1: Protein
Type II secretion system protein D / Type II secretion system / GspD


Mass: 69700.820 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O78:H11 (strain H10407 / ETEC) (bacteria)
Strain: H10407 / ETEC / Gene: ETEC_3237 / Production host: Escherichia coli (E. coli) / References: UniProt: E3PJ86
#2: Protein
Type II secretion system lipoprotein / Type II secretion system / AspS


Mass: 12185.780 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O78:H11 (strain H10407 / ETEC) (bacteria)
Strain: H10407 / ETEC / Gene: ETEC_3239 / Production host: Escherichia coli (E. coli) / References: UniProt: E3PJ88

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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: Pilotin-Secretin Complex Asps-GspD / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli ETEC H10407 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: CTFFIND / Category: CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37928 / Symmetry type: POINT

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