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Yorodumi- PDB-4d3e: Tetramer of IpaD, modified from 2J0O, fitted into negative stain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d3e | ||||||
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Title | Tetramer of IpaD, modified from 2J0O, fitted into negative stain electron microscopy reconstruction of the wild type tip complex from the type III secretion system of Shigella flexneri | ||||||
Components | INVASIN IPAD | ||||||
Keywords | CELL INVASION / TIP COMPLEX / TYPE III SECRETION SYSTEM / SHIGELLA FLEXNERI / WILD TYPE / IPAD | ||||||
Function / homology | Function and homology information effector-mediated activation of programmed cell death in host / extracellular region Similarity search - Function | ||||||
Biological species | SHIGELLA FLEXNERI 5A STR. M90T (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 24 Å | ||||||
Authors | Cheung, M. / Shen, D.-K. / Makino, F. / Kato, T. / Roehrich, D. / Martinez-Argudo, I. / Walker, M.L. / Murillo, I. / Liu, X. / Pain, M. ...Cheung, M. / Shen, D.-K. / Makino, F. / Kato, T. / Roehrich, D. / Martinez-Argudo, I. / Walker, M.L. / Murillo, I. / Liu, X. / Pain, M. / Brown, J. / Frazer, G. / Mantell, J. / Mina, P. / Todd, T. / Sessions, R.B. / Namba, K. / Blocker, A.J. | ||||||
Citation | Journal: Mol Microbiol / Year: 2015 Title: Three-dimensional electron microscopy reconstruction and cysteine-mediated crosslinking provide a model of the type III secretion system needle tip complex. Authors: Martin Cheung / Da-Kang Shen / Fumiaki Makino / Takayuki Kato / A Dorothea Roehrich / Isabel Martinez-Argudo / Matthew L Walker / Isabel Murillo / Xia Liu / Maria Pain / James Brown / Gordon ...Authors: Martin Cheung / Da-Kang Shen / Fumiaki Makino / Takayuki Kato / A Dorothea Roehrich / Isabel Martinez-Argudo / Matthew L Walker / Isabel Murillo / Xia Liu / Maria Pain / James Brown / Gordon Frazer / Judith Mantell / Petros Mina / Thomas Todd / Richard B Sessions / Keiichi Namba / Ariel J Blocker / Abstract: Type III secretion systems are found in many Gram-negative bacteria. They are activated by contact with eukaryotic cells and inject virulence proteins inside them. Host cell detection requires a ...Type III secretion systems are found in many Gram-negative bacteria. They are activated by contact with eukaryotic cells and inject virulence proteins inside them. Host cell detection requires a protein complex located at the tip of the device's external injection needle. The Shigella tip complex (TC) is composed of IpaD, a hydrophilic protein, and IpaB, a hydrophobic protein, which later forms part of the injection pore in the host membrane. Here we used labelling and crosslinking methods to show that TCs from a ΔipaB strain contain five IpaD subunits while the TCs from wild-type can also contain one IpaB and four IpaD subunits. Electron microscopy followed by single particle and helical image analysis was used to reconstruct three-dimensional images of TCs at ∼ 20 Å resolution. Docking of an IpaD crystal structure, constrained by the crosslinks observed, reveals that TC organisation is different from that of all previously proposed models. Our findings suggest new mechanisms for TC assembly and function. The TC is the only site within these secretion systems targeted by disease-protecting antibodies. By suggesting how these act, our work will allow improvement of prophylactic and therapeutic strategies. #1: Journal: J Biol Chem / Year: 2007 Title: Self-chaperoning of the type III secretion system needle tip proteins IpaD and BipD. Authors: Steven Johnson / Pietro Roversi / Marianela Espina / Andrew Olive / Janet E Deane / Susan Birket / Terry Field / William D Picking / Ariel J Blocker / Edouard E Galyov / Wendy L Picking / Susan M Lea / Abstract: Bacteria expressing type III secretion systems (T3SS) have been responsible for the deaths of millions worldwide, acting as key virulence elements in diseases ranging from plague to typhoid fever. ...Bacteria expressing type III secretion systems (T3SS) have been responsible for the deaths of millions worldwide, acting as key virulence elements in diseases ranging from plague to typhoid fever. The T3SS is composed of a basal body, which traverses both bacterial membranes, and an external needle through which effector proteins are secreted. We report multiple crystal structures of two proteins that sit at the tip of the needle and are essential for virulence: IpaD from Shigella flexneri and BipD from Burkholderia pseudomallei. The structures reveal that the N-terminal domains of the molecules are intramolecular chaperones that prevent premature oligomerization, as well as sharing structural homology with proteins involved in eukaryotic actin rearrangement. Crystal packing has allowed us to construct a model for the tip complex that is supported by mutations designed using the structure. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4d3e.cif.gz | 160.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d3e.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 4d3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d3e_validation.pdf.gz | 703.4 KB | Display | wwPDB validaton report |
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Full document | 4d3e_full_validation.pdf.gz | 777 KB | Display | |
Data in XML | 4d3e_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 4d3e_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/4d3e ftp://data.pdbj.org/pub/pdb/validation_reports/d3/4d3e | HTTPS FTP |
-Related structure data
Related structure data | 2801MC 2802C 2803C 2804C 2805C 2806C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Number of models | 4 |
-Components
#1: Protein | Mass: 23076.775 Da / Num. of mol.: 1 Fragment: COILDED-COIL AND GLOBULAR DOMAIN, UNP RESIDUES 125-332 Source method: isolated from a genetically manipulated source Details: YES [LACKING FIRST 124 AA AND WITH LAST 10 AA MODELLED INTO HELIX] Source: (gene. exp.) SHIGELLA FLEXNERI 5A STR. M90T (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P18013 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: WILD-TYPE T3SS NEEDLE COMPLEX / Type: COMPLEX / Details: FIRST ZERO OF CTF SET TO 19A FOR ALL MICROGRAPHS |
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Buffer solution | Name: 0.1% (W/V) DDM, 150 MM NACL, 25 MM TRIS PH 8, 5 MM EDTA pH: 8 Details: 0.1% (W/V) DDM, 150 MM NACL, 25 MM TRIS PH 8, 5 MM EDTA |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO |
EM staining | Type: NEGATIVE / Material: uranyl acetate |
Specimen support | Details: CARBON |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 20 / Date: Aug 31, 2011 |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 70754 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm / Cs: 2 mm |
Image recording | Electron dose: 90 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k) |
Image scans | Num. digital images: 300 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Method: MIX OF SINGLE PARTICLE AND HELICAL RECONSTRUCTION METHODS Resolution: 24 Å / Num. of particles: 2963 / Actual pixel size: 2.12 Å Details: THIS MODEL IS RESULT OF RIGID-BODY TRANSFORMATION OF AN EXISTING PDB MODEL, CONSTRAINED BY A 24 A RESOLUTION EM MAP AND SOME CYSTEINE-MEDIATED CROSSLINKING DATA. THEREFORE, IT DOES NOT ...Details: THIS MODEL IS RESULT OF RIGID-BODY TRANSFORMATION OF AN EXISTING PDB MODEL, CONSTRAINED BY A 24 A RESOLUTION EM MAP AND SOME CYSTEINE-MEDIATED CROSSLINKING DATA. THEREFORE, IT DOES NOT SUPPORT ATOMISTIC INTERPRETATIONS BECAUSE OF LACK OF RESOLUTION. Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Details: METHOD--SEE PUBLICATION REFINEMENT PROTOCOL--X-RAY | ||||||||||||||||
Atomic model building | PDB-ID: 2J0O Accession code: 2J0O / Source name: PDB / Type: experimental model | ||||||||||||||||
Refinement | Highest resolution: 24 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.12 Å
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