[English] 日本語
Yorodumi
- EMDB-28957: Cryo-EM structure of the Agrobacterium T-pilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28957
TitleCryo-EM structure of the Agrobacterium T-pilus
Map data
Sample
  • Complex: T-pilus
    • Organelle or cellular component: VirB2
      • Protein or peptide: Protein virB2
    • Organelle or cellular component: Phosphatidylglycerol 16:1/18:1
  • Ligand: (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
KeywordsVirB/D4 T4SS / Bacterial conjugation / T-pilus / helical filament / PROTEIN FIBRIL
Function / homologyConjugal 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 speciesAgrobacterium tumefaciens (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsKreida S / Narita A / Johnson MD / Tocheva EI / Das A / Jensen GJ / Ghosal D
Funding support United States, Australia, Canada, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI127401 United States
National Health and Medical Research Council (NHMRC, Australia)APP1196924 Australia
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN 04345 Canada
CitationJournal: 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
DepositionNov 27, 2022-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28957.png

Downloads & links

-
Map

FileDownload / File: emd_28957.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.041824292 - 0.06753963
Average (Standard dev.)0.00012728001 (±0.0022377584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_28957_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_28957_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_28957_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : T-pilus

EntireName: T-pilus
Components
  • Complex: T-pilus
    • Organelle or cellular component: VirB2
      • Protein or peptide: Protein virB2
    • Organelle or cellular component: Phosphatidylglycerol 16:1/18:1
  • Ligand: (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

-
Supramolecule #1: T-pilus

SupramoleculeName: T-pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Agrobacterium tumefaciens (bacteria) / Strain: NT1REB(pJK270)
Molecular weightTheoretical: 2.787 kDa/nm

-
Supramolecule #2: VirB2

SupramoleculeName: VirB2 / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Agrobacterium tumefaciens (bacteria) / Strain: NT1REB(pJK270)

-
Supramolecule #3: Phosphatidylglycerol 16:1/18:1

SupramoleculeName: Phosphatidylglycerol 16:1/18:1 / type: organelle_or_cellular_component / ID: 3 / Parent: 1
Source (natural)Organism: Agrobacterium tumefaciens (bacteria) / Strain: NT1REB(pJK270)

-
Macromolecule #1: Protein virB2

MacromoleculeName: Protein virB2 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium tumefaciens (bacteria) / Strain: NT1REB(pJK270)
Molecular weightTheoretical: 12.326439 KDa
SequenceString:
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-...

MacromoleculeName: (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
Molecular weightTheoretical: 746.991 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration1 mg/mL
BufferpH: 5.5 / Component - Concentration: 50.0 mM / Component - Formula: MES / Component - Name: 2-(N-morpholino)ethanesulfonic acid
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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

+
Image processing

Final reconstructionNumber classes used: 2
Applied symmetry - Helical parameters - Δz: 13.44 Å
Applied symmetry - Helical parameters - Δ&Phi: 32.62 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0beta2) / Number images used: 3543
Segment selectionNumber selected: 10934 / Software - Name: RELION (ver. 4.0beta2)
Details: Filaments were manually picked using EMAN2 e2helixboxer and particles were extracted by RELION.
Startup modelType of model: OTHER
Details: A cylinder generated by relion_helix_toolbox, a program in RELION.
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 4.0beta2)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more