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- PDB-3j0r: Model of a type III secretion system needle based on a 7 Angstrom... -

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Basic information

Entry
Database: PDB / ID: 3j0r
TitleModel of a type III secretion system needle based on a 7 Angstrom resolution cryoEM map
ComponentsProtein mxiH
KeywordsPROTEIN TRANSPORT / helical assembly
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / cell surface / extracellular region / identical protein binding
Similarity search - Function
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
Similarity search - Domain/homology
Type 3 secretion system needle filament protein
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsFujii, T. / Cheung, M. / Blanco, A. / Kato, T. / Blocker, A.J. / Namba, K.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Structure of a type III secretion needle at 7-Å resolution provides insights into its assembly and signaling mechanisms.
Authors: Takashi Fujii / Martin Cheung / Amandine Blanco / Takayuki Kato / Ariel J Blocker / Keiichi Namba /
Abstract: Type III secretion systems of Gram-negative bacteria form injection devices that deliver effector proteins into eukaryotic cells during infection. They span both bacterial membranes and the ...Type III secretion systems of Gram-negative bacteria form injection devices that deliver effector proteins into eukaryotic cells during infection. They span both bacterial membranes and the extracellular space to connect with the host cell plasma membrane. Their extracellular portion is a needle-like, hollow tube that serves as a secretion conduit for effector proteins. The needle of Shigella flexneri is approximately 50-nm long and 7-nm thick and is made by the helical assembly of one protein, MxiH. We provide a 7-Å resolution 3D image reconstruction of the Shigella needle by electron cryomicroscopy, which resolves α-helices and a β-hairpin that has never been observed in the crystal and solution structures of needle proteins, including MxiH. An atomic model of the needle based on the 3D-density map, in comparison with that of the bacterial-flagellar filament, provides insights into how such a thin tubular structure is stably assembled by intricate intermolecular interactions. The map also illuminates how the needle-length control protein functions as a ruler within the central channel during export of MxiH for assembly at the distal end of the needle, and how the secretion-activation signal may be transduced through a conformational change of the needle upon host-cell contact.
History
DepositionNov 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2Mar 21, 2012Group: Other
Revision 1.3Apr 4, 2012Group: Database references
Revision 1.4Feb 21, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / em_single_particle_entity / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-5352
  • Imaged by UCSF Chimera
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  • Superimposition on EM map
  • EMDB-5352
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Protein mxiH


Theoretical massNumber of molelcules
Total (without water)9,1411
Polymers9,1411
Non-polymers00
Water0
1
A: Protein mxiH
x 22


Theoretical massNumber of molelcules
Total (without water)201,10322
Polymers201,10322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation21
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 22 / Rise per n subunits: 4.3 Å / Rotation per n subunits: 64.06 °)

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Components

#1: Protein Protein mxiH / type III secretion needle


Mass: 9141.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Shigella flexneri (bacteria) / References: UniProt: P0A223

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: type III secretion needleType three secretion system / Type: COMPLEX / Details: a helical assembly of MxiH
Buffer solutionName: 20 mM Tris, pH 7.4, 150 mM NaCl, 2mM MgSO4 / pH: 7.4 / Details: 20 mM Tris, pH 7.4, 150 mM NaCl, 2mM MgSO4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil holey carbon molybdenum grid (R0.6/1.0, Quantifoil)
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: Blot for 3.5 seconds before plunging into liquid ethane (Vitrobot).

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Jul 2, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 89285 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 1.6 mm
Specimen holderTemperature: 50 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)

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Processing

CTF correctionDetails: CTFFIND3 Each particle
Helical symmertyAngular rotation/subunit: 64.06 ° / Axial rise/subunit: 4.3 Å / Axial symmetry: C1
3D reconstructionMethod: Projection Matching / Resolution: 7.7 Å / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms644 0 0 0 644

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