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- EMDB-2368: Negative-staining electron microscopy structure of the Agrobacter... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2368 | |||||||||
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Title | Negative-staining electron microscopy structure of the Agrobacterium tumefaciens T-complex, composed of the protein VirE2 coating single-stranded DNA. | |||||||||
![]() | Negative-staining EM reconstruction of the Agrobacterium T-complex | |||||||||
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![]() | T-complex / agrobacterium / helical reconstruction / negative staining | |||||||||
Biological species | ![]() | |||||||||
Method | helical reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
![]() | Abu-Arish A / Frenkiel-Krispin D / Fricke T / Tzfira T / Citovsky V / Wolf SG / Elbaum M | |||||||||
![]() | ![]() Title: Three-dimensional reconstruction of Agrobacterium VirE2 protein with single-stranded DNA. Authors: Asmahan Abu-Arish / Daphna Frenkiel-Krispin / Tobin Fricke / Tzvi Tzfira / Vitaly Citovsky / Sharon Grayer Wolf / Michael Elbaum / ![]() Abstract: Agrobacterium tumefaciens infects plant cells by a unique mechanism involving an interkingdom genetic transfer. A single-stranded DNA substrate is transported across the two cell walls along with the ...Agrobacterium tumefaciens infects plant cells by a unique mechanism involving an interkingdom genetic transfer. A single-stranded DNA substrate is transported across the two cell walls along with the bacterial virulence proteins VirD2 and VirE2. A single VirD2 molecule covalently binds to the 5'-end of the single-stranded DNA, while the VirE2 protein binds stoichiometrically along the length of the DNA, without sequence specificity. An earlier transmission/scanning transmission electron microscopy study indicated a solenoidal ("telephone coil") organization of the VirE2-DNA complex. Here we report a three-dimensional reconstruction of this complex using electron microscopy and single-particle image-processing methods. We find a hollow helical structure of 15.7-nm outer diameter, with a helical rise of 51.5 nm and 4.25 VirE2 proteins/turn. The inner face of the protein units contains a continuous wall and an inward protruding shelf. These structures appear to accommodate the DNA binding. Such a quaternary arrangement naturally sequesters the DNA from cytoplasmic nucleases and suggests a mechanism for its nuclear import by decoration with host cell factors. Coexisting with the helices, we also found VirE2 tetrameric ring structures. A two-dimensional average of the latter confirms the major features of the three-dimensional reconstruction. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.3 KB 9.3 KB | Display Display | ![]() |
Images | ![]() | 97.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 223.7 KB | Display | ![]() |
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Full document | ![]() | 222.8 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative-staining EM reconstruction of the Agrobacterium T-complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Negative-staining recosntruction of the Agrobacterium T-complex
Entire | Name: Negative-staining recosntruction of the Agrobacterium T-complex |
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Components |
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-Supramolecule #1000: Negative-staining recosntruction of the Agrobacterium T-complex
Supramolecule | Name: Negative-staining recosntruction of the Agrobacterium T-complex type: sample / ID: 1000 / Details: Helical assembly / Oligomeric state: Helical / Number unique components: 2 |
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-Macromolecule #1: Agrobacterium tumefaciens VirE2 protein
Macromolecule | Name: Agrobacterium tumefaciens VirE2 protein / type: protein_or_peptide / ID: 1 Details: Negative-staining EM reconstruction of the Agrobacterium T-complex Oligomeric state: Helical / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 58 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #2: short oligomeric 26mer DNA
Macromolecule | Name: short oligomeric 26mer DNA / type: dna / ID: 2 / Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: Yes |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Staining | Type: NEGATIVE / Details: 1.5% Uranyl acetate staining |
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Grid | Details: Carbon coated grids |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
Details | Protein was mixed with M13 circular single-stranded DNA. |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Jan 1, 2004 |
Image recording | Category: CCD / Film or detector model: GENERIC TVIPS |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.6 µm |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Details | Helical reconstruction using IHRSR |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 12.11 Å Applied symmetry - Helical parameters - Δ&Phi: 84.7 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Software - Name: Bsoft, Spider, IHRSR |
CTF correction | Details: Phase-flipping |