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- PDB-8axk: Type 3 secretion system export apparatus core, inner rod and need... -

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Basic information

Entry
Database: PDB / ID: 8axk
TitleType 3 secretion system export apparatus core, inner rod and needle of Shigella flexneri
Components
  • (Surface presentation of antigens protein ...) x 4
  • Lipoprotein MxiJ
  • Outer membrane protein MxiD
  • Protein MxiH
  • Protein MxiI
KeywordsPROTEIN TRANSPORT / type 3 secretion / needle complex / virulence factor / shigella / infection
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / protein secretion / protein targeting / cell outer membrane / protein transport / cell surface / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / Type III secretion protein SpaR/YscT / Type III secretion protein HrpO / Yop virulence translocation protein R / Type III exporter system, secretion apparatus protein BsaZ / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / Type III secretion system lipoprotein HrcJ/YscJ / : ...: / Type III secretion protein SpaR/YscT / Type III secretion protein HrpO / Yop virulence translocation protein R / Type III exporter system, secretion apparatus protein BsaZ / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / Type III secretion system lipoprotein HrcJ/YscJ / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2. / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Surface presentation of antigens protein SpaP / Surface presentation of antigens protein SpaQ / Surface presentation of antigens protein SpaR / Surface presentation of antigens protein SpaS / Type 3 secretion system needle filament protein / Protein MxiI / Type 3 secretion system secretin / Lipoprotein MxiJ
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsLunelli, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: Protein Sci / Year: 2023
Title: Integrative structural analysis of the type III secretion system needle complex from Shigella flexneri.
Authors: Lara Flacht / Michele Lunelli / Karol Kaszuba / Zhuo Angel Chen / Francis J O' Reilly / Juri Rappsilber / Jan Kosinski / Michael Kolbe /
Abstract: The type III secretion system (T3SS) is a large, transmembrane protein machinery used by various pathogenic gram-negative bacteria to transport virulence factors into the host cell during infection. ...The type III secretion system (T3SS) is a large, transmembrane protein machinery used by various pathogenic gram-negative bacteria to transport virulence factors into the host cell during infection. Understanding the structure of T3SSs is crucial for future developments of therapeutics that could target this system. However, much of the knowledge about the structure of T3SS is available only for Salmonella, and it is unclear how this large assembly is conserved across species. Here, we combined cryo-electron microscopy, cross-linking mass spectrometry, and integrative modeling to determine the structure of the T3SS needle complex from Shigella flexneri. We show that the Shigella T3SS exhibits unique features distinguishing it from other structurally characterized T3SSs. The secretin pore complex adopts a new fold of its C-terminal S domain and the pilotin MxiM[SctG] locates around the outer surface of the pore. The export apparatus structure exhibits a conserved pseudohelical arrangement but includes the N-terminal domain of the SpaS[SctU] subunit, which was not present in any of the previously published virulence-related T3SS structures. Similar to other T3SSs, however, the apparatus is anchored within the needle complex by a network of flexible linkers that either adjust conformation to connect to equivalent patches on the secretin oligomer or bind distinct surface patches at the same height of the export apparatus. The conserved and unique features delineated by our analysis highlight the necessity to analyze T3SS in a species-specific manner, in order to fully understand the underlying molecular mechanisms of these systems. The structure of the type III secretion system from Shigella flexneri delineates conserved and unique features, which could be used for the development of broad-range therapeutics.
History
DepositionAug 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / em_entity_assembly_molwt / pdbx_entry_details / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _em_entity_assembly_molwt.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Surface presentation of antigens protein SpaP
B: Surface presentation of antigens protein SpaP
C: Surface presentation of antigens protein SpaP
D: Surface presentation of antigens protein SpaP
E: Surface presentation of antigens protein SpaP
F: Surface presentation of antigens protein SpaR
G: Surface presentation of antigens protein SpaQ
H: Surface presentation of antigens protein SpaQ
I: Surface presentation of antigens protein SpaQ
J: Surface presentation of antigens protein SpaQ
K: Surface presentation of antigens protein SpaS
M: Protein MxiI
N: Protein MxiI
O: Protein MxiI
P: Protein MxiI
Q: Protein MxiI
R: Protein MxiI
S: Protein MxiH
T: Protein MxiH
U: Protein MxiH
V: Protein MxiH
W: Protein MxiH
X: Outer membrane protein MxiD
Y: Outer membrane protein MxiD
Z: Outer membrane protein MxiD
0: Outer membrane protein MxiD
2: Outer membrane protein MxiD
4: Outer membrane protein MxiD
6: Outer membrane protein MxiD
8: Outer membrane protein MxiD
x: Outer membrane protein MxiD
y: Outer membrane protein MxiD
z: Outer membrane protein MxiD
1: Outer membrane protein MxiD
3: Outer membrane protein MxiD
5: Outer membrane protein MxiD
7: Outer membrane protein MxiD
9: Outer membrane protein MxiD
a: Protein MxiH
b: Protein MxiH
c: Protein MxiH
d: Protein MxiH
e: Protein MxiH
f: Protein MxiH
g: Protein MxiH
h: Protein MxiH
i: Protein MxiH
j: Protein MxiH
k: Protein MxiH
l: Protein MxiH
m: Protein MxiH
n: Protein MxiH
o: Protein MxiH
p: Protein MxiH
q: Protein MxiH
r: Protein MxiH
s: Protein MxiH
t: Protein MxiH
u: Protein MxiH
v: Protein MxiH
w: Protein MxiH
a0: Lipoprotein MxiJ
b0: Lipoprotein MxiJ
c0: Lipoprotein MxiJ
d0: Lipoprotein MxiJ
e0: Lipoprotein MxiJ
f0: Lipoprotein MxiJ
g0: Lipoprotein MxiJ
h0: Lipoprotein MxiJ
i0: Lipoprotein MxiJ
j0: Lipoprotein MxiJ
k0: Lipoprotein MxiJ
l0: Lipoprotein MxiJ
m0: Lipoprotein MxiJ
n0: Lipoprotein MxiJ
o0: Lipoprotein MxiJ
p0: Lipoprotein MxiJ
q0: Lipoprotein MxiJ
r0: Lipoprotein MxiJ
s0: Lipoprotein MxiJ
t0: Lipoprotein MxiJ
u0: Lipoprotein MxiJ
v0: Lipoprotein MxiJ
w0: Lipoprotein MxiJ
x0: Lipoprotein MxiJ


Theoretical massNumber of molelcules
Total (without water)2,273,45285
Polymers2,273,45285
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area213230 Å2
ΔGint-1658 kcal/mol
Surface area224710 Å2
MethodPISA

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Components

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Surface presentation of antigens protein ... , 4 types, 11 molecules ABCDEFGHIJK

#1: Protein
Surface presentation of antigens protein SpaP / Spa24 protein


Mass: 24215.562 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Shigella flexneri (bacteria) / References: UniProt: P0A1L3
#2: Protein Surface presentation of antigens protein SpaR / Spa29 protein


Mass: 28513.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Shigella flexneri (bacteria) / References: UniProt: P0A1M6
#3: Protein
Surface presentation of antigens protein SpaQ / Protein spa9


Mass: 9433.338 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Shigella flexneri (bacteria) / References: UniProt: P0A1M4
#4: Protein Surface presentation of antigens protein SpaS / Spa40 protein


Mass: 39903.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Shigella flexneri (bacteria) / References: UniProt: P0A1M8

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Protein , 4 types, 74 molecules MNOPQRSTUVWabcdefghijklmnopqrs...

#5: Protein
Protein MxiI


Mass: 10640.000 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Shigella flexneri (bacteria) / References: UniProt: P0A225
#6: Protein ...
Protein MxiH


Mass: 11060.279 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: mxiH, CP0137 / Plasmid: pASK-IBA5plus / Production host: Shigella flexneri (bacteria) / References: UniProt: P0A223
#7: Protein
Outer membrane protein MxiD


Mass: 63230.414 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Shigella flexneri (bacteria) / References: UniProt: Q04641
#8: Protein ...
Lipoprotein MxiJ


Mass: 27542.055 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Shigella flexneri (bacteria) / References: UniProt: Q06081

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Details

Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Needle complex of the type 3 secretion systemCOMPLEXall0NATURAL
2Export apparatus coreCOMPLEX#1-#41NATURAL
3Inner rodCOMPLEX#51NATURAL
4Needle filamentCOMPLEX#61NATURAL
5Ring formed by the N1 domain of the secretin MxiDCOMPLEX#71NATURAL
6MxiJ loop interacting with the export apparatusCOMPLEX#81NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11
22
33
44
55NO
66NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Shigella flexneri (bacteria)623
32Shigella flexneri (bacteria)623
43Shigella flexneri (bacteria)623
54Shigella flexneri (bacteria)623
65Shigella flexneri (bacteria)623
76Shigella flexneri (bacteria)623
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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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 FIELD / Nominal magnification: 101179 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5238
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 1-6

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1.13CTF correction
7UCSF Chimera1.15model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
12RELION33D reconstruction
13PHENIX1.18.2_3874model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90547 / Symmetry type: POINT
Atomic model buildingB value: 59.2 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16RWY

6rwy

16RWY1PDBexperimental model
26RWK

6rwk

16RWK2PDBexperimental model
36RWX

6rwx

16RWX3PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00244858
ELECTRON MICROSCOPYf_angle_d0.43460890
ELECTRON MICROSCOPYf_dihedral_angle_d13.27116522
ELECTRON MICROSCOPYf_chiral_restr0.0367369
ELECTRON MICROSCOPYf_plane_restr0.0047620

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