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- PDB-6uot: Cryo-EM structure of the PrgHK periplasmic ring from the Salmonel... -

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Basic information

Entry
Database: PDB / ID: 6uot
TitleCryo-EM structure of the PrgHK periplasmic ring from the Salmonella SPI-1 type III secretion needle complex solved at 3.3 angstrom resolution
Components
  • Lipoprotein PrgK
  • Protein PrgH
KeywordsMEMBRANE PROTEIN / BACTERIAL NANOMACHINE / TYPE III SECRETION SYSTEM
Function / homology
Function and homology information


protein secretion / cell outer membrane / plasma membrane
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #170 / Alpha-Beta Plaits - #1780 / Alpha-Beta Plaits - #1770 / Type III secretion system, PrgH/EprH / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal ...GMP Synthetase; Chain A, domain 3 - #170 / Alpha-Beta Plaits - #1780 / Alpha-Beta Plaits - #1770 / Type III secretion system, PrgH/EprH / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein PrgH / Lipoprotein PrgK
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsButan, C. / Galan, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: High-resolution view of the type III secretion export apparatus in situ reveals membrane remodeling and a secretion pathway.
Authors: Carmen Butan / Maria Lara-Tejero / Wenwei Li / Jun Liu / Jorge E Galán /
Abstract: Type III protein secretion systems are essential virulence factors for many important pathogenic bacteria. The entire protein secretion machine is composed of several substructures that organize into ...Type III protein secretion systems are essential virulence factors for many important pathogenic bacteria. The entire protein secretion machine is composed of several substructures that organize into a holostructure or injectisome. The core component of the injectisome is the needle complex, which houses the export apparatus that serves as a gate for the passage of the secreted proteins through the bacterial inner membrane. Here, we describe a high-resolution structure of the export apparatus of the type III secretion system in association with the needle complex and the underlying bacterial membrane, both in isolation and in situ. We show the precise location of the core export apparatus components within the injectisome and bacterial envelope and demonstrate that their deployment results in major membrane remodeling and thinning, which may be central for the protein translocation process. We also show that InvA, a critical export apparatus component, forms a multiring cytoplasmic conduit that provides a pathway for the type III secretion substrates to reach the entrance of the export gate. Combined with structure-guided mutagenesis, our studies provide major insight into potential mechanisms of protein translocation and injectisome assembly.
History
DepositionOct 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 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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Assembly

Deposited unit
A: Protein PrgH
B: Protein PrgH
C: Protein PrgH
D: Protein PrgH
E: Protein PrgH
F: Protein PrgH
G: Protein PrgH
H: Protein PrgH
I: Protein PrgH
J: Protein PrgH
K: Protein PrgH
L: Protein PrgH
M: Protein PrgH
N: Protein PrgH
O: Protein PrgH
P: Protein PrgH
Q: Protein PrgH
R: Protein PrgH
S: Protein PrgH
T: Protein PrgH
U: Protein PrgH
V: Protein PrgH
W: Protein PrgH
X: Protein PrgH
Y: Lipoprotein PrgK
Z: Lipoprotein PrgK
a: Lipoprotein PrgK
b: Lipoprotein PrgK
c: Lipoprotein PrgK
d: Lipoprotein PrgK
e: Lipoprotein PrgK
f: Lipoprotein PrgK
g: Lipoprotein PrgK
h: Lipoprotein PrgK
i: Lipoprotein PrgK
j: Lipoprotein PrgK
k: Lipoprotein PrgK
l: Lipoprotein PrgK
m: Lipoprotein PrgK
n: Lipoprotein PrgK
o: Lipoprotein PrgK
p: Lipoprotein PrgK
q: Lipoprotein PrgK
r: Lipoprotein PrgK
s: Lipoprotein PrgK
t: Lipoprotein PrgK
u: Lipoprotein PrgK
v: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)1,746,11248
Polymers1,746,11248
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Protein PrgH


Mass: 44509.367 Da / Num. of mol.: 24 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P41783
#2: Protein ...
Lipoprotein PrgK


Mass: 28245.287 Da / Num. of mol.: 24 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P41786

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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 the periplasmic domains of PrgH and PrgK from the Salmonella SPI-1 type III secretion needle complex
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELDBright-field microscopy
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
PHENIX(1.14rc1_3161:phenix.real_space_refine)refinement
PDB_EXTRACT3.25data extraction
EM software
IDNameVersionCategory
1RELION2.1particle selection
4CTFFIND4CTF correction
9PHENIXmodel refinement
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C24 (24 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23433 / Symmetry type: POINT
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 95.39 Å2 / Biso mean: 46.29 Å2 / Biso min: 25.37 Å2

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