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- PDB-8exh: Agrobacterium tumefaciens Tpilus -

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Basic information

Entry
Database: PDB / ID: 8exh
TitleAgrobacterium tumefaciens Tpilus
ComponentsProtein virB2
KeywordsPROTEIN FIBRIL / T-pilus
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 / Chem-X3D / Protein virB2
Function and homology information
Biological speciesAgrobacterium fabrum (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / negative staining / cryo EM / Resolution: 3.5 Å
AuthorsBeltran, L.C. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Nat Commun / Year: 2023
Title: Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery.
Authors: Leticia C Beltran / Virginija Cvirkaite-Krupovic / Jessalyn Miller / Fengbin Wang / Mark A B Kreutzberger / Jonasz B Patkowski / Tiago R D Costa / Stefan Schouten / Ilya Levental / Vincent P ...Authors: Leticia C Beltran / Virginija Cvirkaite-Krupovic / Jessalyn Miller / Fengbin Wang / Mark A B Kreutzberger / Jonasz B Patkowski / Tiago R D Costa / Stefan Schouten / Ilya Levental / Vincent P Conticello / Edward H Egelman / Mart Krupovic /
Abstract: Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient ...Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been 'domesticated', that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.
History
DepositionOct 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Sep 25, 2024Group: Data collection / Experimental preparation / Category: em_admin / em_staining / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein virB2
B: Protein virB2
C: Protein virB2
D: Protein virB2
E: Protein virB2
F: Protein virB2
G: Protein virB2
H: Protein virB2
I: Protein virB2
J: Protein virB2
K: Protein virB2
L: Protein virB2
M: Protein virB2
N: Protein virB2
O: Protein virB2
P: Protein virB2
Q: Protein virB2
R: Protein virB2
S: Protein virB2
T: Protein virB2
U: Protein virB2
V: Protein virB2
W: Protein virB2
X: Protein virB2
Y: Protein virB2
Z: Protein virB2
a: Protein virB2
b: Protein virB2
c: Protein virB2
d: Protein virB2
e: Protein virB2
f: Protein virB2
g: Protein virB2
h: Protein virB2
i: Protein virB2
j: Protein virB2
k: Protein virB2
l: Protein virB2
m: Protein virB2
n: Protein virB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,87380
Polymers272,12240
Non-polymers23,75140
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Protein virB2


Mass: 6803.045 Da / Num. of mol.: 40 / Source method: isolated from a natural source
Source: (natural) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / References: UniProt: P17792
#2: Chemical...
ChemComp-X3D / (14S,17R)-20-amino-17-hydroxy-11,17-dioxo-12,16,18-trioxa-17lambda~5~-phosphaicosan-14-yl tetradecanoate


Mass: 593.773 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C30H60NO8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: T-pilus Filament (VirB2 pilin subunit) / Type: ORGANELLE OR CELLULAR COMPONENT / Details: Filaments generated by shearing off of bacteria / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Agrobacterium fabrum str. C58 (bacteria) / Cellular location: extracellular
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
Specimen supportGrid type: EMS Lacey Carbon
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K / Details: blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM softwareName: cryoSPARC / Version: 3.1 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 32.45 ° / Axial rise/subunit: 13.68 Å / Axial symmetry: C5
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49308 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00220920
ELECTRON MICROSCOPYf_angle_d2.5527960
ELECTRON MICROSCOPYf_dihedral_angle_d16.38111760
ELECTRON MICROSCOPYf_chiral_restr0.0363240
ELECTRON MICROSCOPYf_plane_restr0.0033320

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