+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28957 | ||||||||||||
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Title | Cryo-EM structure of the Agrobacterium T-pilus | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | VirB/D4 T4SS / Bacterial conjugation / T-pilus / helical filament / PROTEIN FIBRIL | ||||||||||||
Function / homology | Conjugal transfer TrbC/type IV secretion VirB2 / TrbC/VIRB2 pilin / type IV secretion system complex / protein secretion by the type IV secretion system / cell outer membrane / Protein virB2 Function and homology information | ||||||||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||
Authors | Kreida S / Narita A / Johnson MD / Tocheva EI / Das A / Jensen GJ / Ghosal D | ||||||||||||
Funding support | United States, Australia, Canada, 3 items
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Citation | Journal: Structure / Year: 2023 Title: Cryo-EM structure of the Agrobacterium tumefaciens T4SS-associated T-pilus reveals stoichiometric protein-phospholipid assembly. Authors: Stefan Kreida / Akihiro Narita / Matthew D Johnson / Elitza I Tocheva / Anath Das / Debnath Ghosal / Grant J Jensen / Abstract: Agrobacterium tumefaciens causes crown gall disease in plants by the horizontal transfer of oncogenic DNA. The conjugation is mediated by the VirB/D4 type 4 secretion system (T4SS) that assembles an ...Agrobacterium tumefaciens causes crown gall disease in plants by the horizontal transfer of oncogenic DNA. The conjugation is mediated by the VirB/D4 type 4 secretion system (T4SS) that assembles an extracellular filament, the T-pilus, and is involved in mating pair formation between A. tumefaciens and the recipient plant cell. Here, we present a 3 Å cryoelectron microscopy (cryo-EM) structure of the T-pilus solved by helical reconstruction. Our structure reveals that the T-pilus is a stoichiometric assembly of the VirB2 major pilin and phosphatidylglycerol (PG) phospholipid with 5-start helical symmetry. We show that PG head groups and the positively charged Arg 91 residues of VirB2 protomers form extensive electrostatic interactions in the lumen of the T-pilus. Mutagenesis of Arg 91 abolished pilus formation. While our T-pilus structure is architecturally similar to previously published conjugative pili structures, the T-pilus lumen is narrower and positively charged, raising questions of whether the T-pilus is a conduit for ssDNA transfer. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28957.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-28957-v30.xml emd-28957.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28957_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_28957.png | 143.5 KB | ||
Masks | emd_28957_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-28957.cif.gz | 5.8 KB | ||
Others | emd_28957_half_map_1.map.gz emd_28957_half_map_2.map.gz | 80.7 MB 80.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28957 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28957 | HTTPS FTP |
-Validation report
Summary document | emd_28957_validation.pdf.gz | 983.7 KB | Display | EMDB validaton report |
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Full document | emd_28957_full_validation.pdf.gz | 983.3 KB | Display | |
Data in XML | emd_28957_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | emd_28957_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28957 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28957 | HTTPS FTP |
-Related structure data
Related structure data | 8faiMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28957.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28957_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28957_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28957_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : T-pilus
Entire | Name: T-pilus |
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Components |
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-Supramolecule #1: T-pilus
Supramolecule | Name: T-pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Agrobacterium tumefaciens (bacteria) / Strain: NT1REB(pJK270) |
Molecular weight | Theoretical: 2.787 kDa/nm |
-Supramolecule #2: VirB2
Supramolecule | Name: VirB2 / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Agrobacterium tumefaciens (bacteria) / Strain: NT1REB(pJK270) |
-Supramolecule #3: Phosphatidylglycerol 16:1/18:1
Supramolecule | Name: Phosphatidylglycerol 16:1/18:1 / type: organelle_or_cellular_component / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Agrobacterium tumefaciens (bacteria) / Strain: NT1REB(pJK270) |
-Macromolecule #1: Protein virB2
Macromolecule | Name: Protein virB2 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO |
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Source (natural) | Organism: Agrobacterium tumefaciens (bacteria) / Strain: NT1REB(pJK270) |
Molecular weight | Theoretical: 12.326439 KDa |
Sequence | String: MRCFERYRVH LNRLSLSNAV MRMVSGYAPS VVGAMGWSIF SSGPAAAQSA GGGTDPATMV NNICTFILGP FGQSLAVLGI VAIGISWMF GRASLGLVAG VVGGIVIMFG ASFLGKTLTG GG UniProtKB: Protein virB2 |
-Macromolecule #2: (7Z,19R,22S,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-...
Macromolecule | Name: (7Z,19R,22S,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacos-7-en-19-yl (9Z)-octadec-9-enoate type: ligand / ID: 2 / Number of copies: 15 / Formula: XL0 |
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Molecular weight | Theoretical: 746.991 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 5.5 / Component - Concentration: 50.0 mM / Component - Formula: MES / Component - Name: 2-(N-morpholino)ethanesulfonic acid |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |