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- PDB-8u2b: Cryo-EM structure of C.crescentus bNY30a pilus complex -

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Basic information

Entry
Database: PDB / ID: 8u2b
TitleCryo-EM structure of C.crescentus bNY30a pilus complex
ComponentsFlp family type IVb pilin
KeywordsPROTEIN FIBRIL / Complex
Function / homologyFlp/Fap pilin component / Flp/Fap pilin component / membrane / Flp family type IVb pilin
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWang, Y. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R01GM141659 United States
CitationJournal: Sci Adv / Year: 2024
Title: Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus.
Authors: Yuhang Wang / Matthew Theodore / Zhongliang Xing / Utkarsh Narsaria / Zihao Yu / Lanying Zeng / Junjie Zhang /
Abstract: Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV ... Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in , maintaining infectivity against , which presents promising applications, including RNA delivery and phage display.
History
DepositionSep 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 17, 2024Group: Data collection / Data processing / Category: em_3d_reconstruction / em_admin
Item: _em_3d_reconstruction.resolution / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flp family type IVb pilin
J: Flp family type IVb pilin
K: Flp family type IVb pilin
L: Flp family type IVb pilin
M: Flp family type IVb pilin
N: Flp family type IVb pilin
O: Flp family type IVb pilin
P: Flp family type IVb pilin
Q: Flp family type IVb pilin
R: Flp family type IVb pilin
S: Flp family type IVb pilin
T: Flp family type IVb pilin
U: Flp family type IVb pilin
V: Flp family type IVb pilin
W: Flp family type IVb pilin
X: Flp family type IVb pilin
Y: Flp family type IVb pilin
Z: Flp family type IVb pilin
a: Flp family type IVb pilin
b: Flp family type IVb pilin
c: Flp family type IVb pilin
d: Flp family type IVb pilin
e: Flp family type IVb pilin
f: Flp family type IVb pilin
g: Flp family type IVb pilin
h: Flp family type IVb pilin
i: Flp family type IVb pilin
j: Flp family type IVb pilin
k: Flp family type IVb pilin
l: Flp family type IVb pilin
m: Flp family type IVb pilin
n: Flp family type IVb pilin
o: Flp family type IVb pilin
p: Flp family type IVb pilin
q: Flp family type IVb pilin
r: Flp family type IVb pilin
s: Flp family type IVb pilin


Theoretical massNumber of molelcules
Total (without water)162,02837
Polymers162,02837
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ...
Flp family type IVb pilin


Mass: 4379.140 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Source: (natural) Caulobacter vibrioides (bacteria) / References: UniProt: A0A290MFS9

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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: Caulobacter crescentus pili / Type: COMPLEX / Details: Caulobacter crescentus pili in buffer / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.17 MDa / Experimental value: NO
Source (natural)Organism: Caulobacter vibrioides (bacteria)
Buffer solutionpH: 7.5 / Details: 20mM tris, 2mM MgCl2
Buffer component
IDConc.NameFormulaBuffer-ID
12 mMMagnesium chlorideMgCl21
220 mMTrisC4H11NO31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/1
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 5000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.17.1_3660: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 51.96 ° / Axial rise/subunit: 14.69 Å / Axial symmetry: C1
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 392496 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00713244
ELECTRON MICROSCOPYf_angle_d0.58818189
ELECTRON MICROSCOPYf_dihedral_angle_d3.6891935
ELECTRON MICROSCOPYf_chiral_restr0.0362795
ELECTRON MICROSCOPYf_plane_restr0.0042064

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