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- PDB-6rwk: MxiD N0 N1 and MxiG C-terminal domains of the Shigella type 3 sec... -

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Basic information

Entry
Database: PDB / ID: 6rwk
TitleMxiD N0 N1 and MxiG C-terminal domains of the Shigella type 3 secretion system
Components
  • Outer membrane protein MxiD
  • Protein MxiG
KeywordsPROTEIN TRANSPORT / type 3 secretion system / shigella / secretin / beta-sheet augmentation
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / cell outer membrane / plasma membrane
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #120 / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site ...Ribosomal Protein S8; Chain: A, domain 1 - #120 / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / 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 / 3-Layer(bab) Sandwich / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein MxiG / Type 3 secretion system secretin
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsKamprad, A. / Lunelli, M.
Funding support2items
OrganizationGrant numberCountry
European Research Council311371
European Union653706
CitationJournal: PLoS Pathog / Year: 2020
Title: Cryo-EM structure of the Shigella type III needle complex.
Authors: Michele Lunelli / Antje Kamprad / Jörg Bürger / Thorsten Mielke / Christian M T Spahn / Michael Kolbe /
Abstract: The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram- ...The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram-negative bacterial pathogens. This system is composed of a membrane-embedded basal body and an extracellular needle that deliver effector proteins into host cells. High-resolution structures of the T3SS from different organisms and infection stages are needed to understand the underlying molecular mechanisms of effector translocation. Here, we present the cryo-electron microscopy structure of the isolated Shigella T3SS needle complex. The inner membrane (IM) region of the basal body adopts 24-fold rotational symmetry and forms a channel system that connects the bacterial periplasm with the export apparatus cage. The secretin oligomer adopts a heterogeneous architecture with 16- and 15-fold cyclic symmetry in the periplasmic N-terminal connector and C-terminal outer membrane ring, respectively. Two out of three IM subunits bind the secretin connector via a β-sheet augmentation. The cryo-EM map also reveals the helical architecture of the export apparatus core, the inner rod, the needle and their intervening interfaces.
History
DepositionJun 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
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 MxiG
D: Protein MxiG
G: Protein MxiG
J: Protein MxiG
M: Protein MxiG
P: Protein MxiG
S: Protein MxiG
U: Protein MxiG
B: Protein MxiG
E: Protein MxiG
H: Protein MxiG
K: Protein MxiG
N: Protein MxiG
Q: Protein MxiG
T: Protein MxiG
V: Protein MxiG


Theoretical massNumber of molelcules
Total (without water)1,700,54832
Polymers1,700,54832
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area61390 Å2
ΔGint-281 kcal/mol
Surface area119050 Å2
MethodPISA

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Components

#1: Protein
Outer membrane protein MxiD


Mass: 63230.414 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Details: MxiD N0 and N1 N-terminal domains in complex with MxiG C-terminal domain
Source: (natural) Shigella flexneri (bacteria) / Variant: M90T / References: UniProt: Q04641
#2: Protein
Protein MxiG


Mass: 43053.844 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Details: MxiG C-terminal domain in complex with secretin MxiD
Source: (natural) Shigella flexneri (bacteria) / References: UniProt: P0A221

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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: Oligomer of the secretin N0 and N1 domains in complex with the inner membrane ring of the Shigella type 3 secretion system
Type: COMPLEX
Details: Focused reconstruction from isolated needle complex of the Shigella type 3 secretion system
Entity ID: all / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Shigella flexneri (bacteria) / Strain: M90T / Cellular location: Membrane
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Isolated needle complex in detergent solution
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: Sample applied on grid 5 ul, incubation time 5 min on ice, then moved into Vitrobot and 5 ul sample applied again. Blot time: 2 sec Blot force: -2 Drain time: 0 sec

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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: 4 nm / Nominal defocus min: 1.5 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 / 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

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Processing

SoftwareName: PHENIX / Version: dev_3357: / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
4CTFFIND3.5CTF correction
7UCSF Chimera1.13.1model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX3357model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 171833
SymmetryPoint symmetry: C8 (8 fold cyclic)
3D reconstructionResolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72298 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 120 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient and geometry
Details: Model was built and refined in the map low-pass filtered at 3.5 A
Atomic model buildingPDB-ID: 3GR5

3gr5


Pdb chain-ID: A / Accession code: 3GR5 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00722224
ELECTRON MICROSCOPYf_angle_d0.74430080
ELECTRON MICROSCOPYf_dihedral_angle_d13.15713248
ELECTRON MICROSCOPYf_chiral_restr0.0463392
ELECTRON MICROSCOPYf_plane_restr0.0053744

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