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- PDB-2v6l: Molecular Model of a Type III Secretion System Needle -

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Basic information

Entry
Database: PDB / ID: 2v6l
TitleMolecular Model of a Type III Secretion System Needle
ComponentsMXIH
KeywordsPROTEIN TRANSPORT / T3SS / VIRULENCE / TRANSPORT
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 / negative staining / Resolution: 16 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 0
AuthorsDeane, J.E. / Roversi, P. / Cordes, F.S. / Johnson, S. / Kenjale, R. / Daniell, S. / Booy, F. / Picking, W.L. / Picking, W.D. / Blocker, A.J. / Lea, S.M.
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2006
Title: Molecular model of a type III secretion system needle: Implications for host-cell sensing.
Authors: Janet E Deane / Pietro Roversi / Frank S Cordes / Steven Johnson / Roma Kenjale / Sarah Daniell / Frank Booy / William D Picking / Wendy L Picking / Ariel J Blocker / Susan M Lea /
Abstract: Type III secretion systems are essential virulence determinants for many Gram-negative bacterial pathogens. The type III secretion system consists of cytoplasmic, transmembrane, and extracellular ...Type III secretion systems are essential virulence determinants for many Gram-negative bacterial pathogens. The type III secretion system consists of cytoplasmic, transmembrane, and extracellular domains. The extracellular domain is a hollow needle protruding above the bacterial surface and is held within a basal body that traverses both bacterial membranes. Effector proteins are translocated, via this external needle, directly into host cells, where they subvert normal cell functions to aid infection. Physical contact with host cells initiates secretion and leads to formation of a pore, thought to be contiguous with the needle channel, in the host-cell membrane. Here, we report the crystal structure of the Shigella flexneri needle subunit MxiH and a complete model for the needle assembly built into our three-dimensional EM reconstruction. The model, combined with mutagenesis data, reveals that signaling of host-cell contact is relayed through the needle via intersubunit contacts and suggests a mode of binding for a tip complex.
#1: Journal: J Biol Chem / Year: 2003
Title: Helical structure of the needle of the type III secretion system of Shigella flexneri.
Authors: Frank S Cordes / Kaoru Komoriya / Eric Larquet / Shixin Yang / Edward H Egelman / Ariel Blocker / Susan M Lea /
Abstract: Gram-negative bacteria commonly interact with animal and plant hosts using type III secretion systems (TTSSs) for translocation of proteins into eukaryotic cells during infection. 10 of the 25 TTSS- ...Gram-negative bacteria commonly interact with animal and plant hosts using type III secretion systems (TTSSs) for translocation of proteins into eukaryotic cells during infection. 10 of the 25 TTSS-encoding genes are homologous to components of the bacterial flagellar basal body, which the TTSS needle complex morphologically resembles. This indicates a common ancestry, although no TTSS sequence homologues for the genes encoding the flagellum are found. We here present an approximately 16-A structure of the central component, the needle, of the TTSS. Although the needle subunit is significantly smaller and shares no sequence homology with the flagellar hook and filament, it shares a common helical architecture ( approximately 5.6 subunits/turn, 24-A helical pitch). This common architecture implies that there will be further mechanistic analogies in the functioning of these two bacterial systems.
History
DepositionJul 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Derived calculations / Other ...Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Aug 2, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_image_scans / em_software
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id ..._em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Assembly

Deposited unit
0: MXIH
1: MXIH
A: MXIH
B: MXIH
C: MXIH
D: MXIH
E: MXIH
F: MXIH
G: MXIH
H: MXIH
I: MXIH
J: MXIH
K: MXIH
L: MXIH
M: MXIH
N: MXIH
O: MXIH
P: MXIH
Q: MXIH
R: MXIH
S: MXIH
T: MXIH
U: MXIH
V: MXIH
W: MXIH
X: MXIH
Y: MXIH
Z: MXIH


Theoretical massNumber of molelcules
Total (without water)259,62328
Polymers259,62328
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

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Components

#1: Protein ...
MXIH / Coordinate model: Cα atoms only


Mass: 9272.265 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Details: RESIDUES 2-19 WERE MODELLED AS AN ALPHA HELIX. RESIDUES 20-80 COME FROM MOLECULE A OF PDB ENTRY 2CA5 RESIDUES 81-85 WERE MODELLED AS AN ALPHA HELIX.
Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Strain: PWR100 / Plasmid: PET22B / Production host: Escherichia coli BL21(DE3) (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: SHIGELLA FLEXNERI TYPE THREE SECRETION NEEDLE / Type: COMPLEX / Details: STAINED WITH A DROP OF 2% URANYL ACETATE, PH 7.5
Buffer solutionName: 10 MM TRIS / pH: 7.5 / Details: 10 MM TRIS
SpecimenConc.: 0.03 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200T / Details: OTHER
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000 X / Nominal defocus max: 700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 10 e/Å2 / Film or detector model: GENERIC FILM
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1BUSTERmodel fitting
2MRC IMAGE PROCESSING PACKAGE3D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: GRID
3D reconstructionMethod: RECIPROCAL SPACE RIGID BODY FIT / Resolution: 16 Å / Num. of particles: 5000 / Nominal pixel size: 2.65 Å
Details: A SET OF X-RAY STRUCTURE FACTORS WERE COMPUTED BY PLACING THE EM DENSITY IN A CRYSTAL CELL. THE MXIH MONOMER WAS RIGID BODY REFINED AGAINST THESE DATA WITH HARD NCS CONSTRAINTS. THE EM ...Details: A SET OF X-RAY STRUCTURE FACTORS WERE COMPUTED BY PLACING THE EM DENSITY IN A CRYSTAL CELL. THE MXIH MONOMER WAS RIGID BODY REFINED AGAINST THESE DATA WITH HARD NCS CONSTRAINTS. THE EM DENSITY FOR THE NEEDLE WAS PUT IN THIS P1 CRYSTAL CELL SO THAT SINGLE CRYSTAL X-RAY MODEL REFINEMENT PROGRAMS COULD BE USED TO FIT THE MODEL.
Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Target criteria: Cross-correlation coefficient
Details: METHOD--RECIPROCAL SPACE FIT REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 2CA5

2ca5

RefinementHighest resolution: 16 Å
Refinement stepCycle: LAST / Highest resolution: 16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 0 0 2296

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