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- PDB-9u5s: The structure of the BfpBG complex in the T4bP system -

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Basic information

Entry
Database: PDB / ID: 9u5s
TitleThe structure of the BfpBG complex in the T4bP system
Components
  • Lipoprotein
  • Outer membrane lipoprotein BfpB
KeywordsPROTEIN TRANSPORT / SECRETIN FAMILY / C17 SYMMETRY / T4bP
Function / homology
Function and homology information


pilus assembly / protein secretion / cell outer membrane
Similarity search - Function
Secretin, N-terminal / Secretin N-terminal domain / Toxin co-regulated pilus biosynthesis protein Q, C-terminal / Toxin co-regulated pilus biosynthesis protein Q / : / Type II/III secretion system / Bacterial type II and III secretion system protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Lipoprotein / Outer membrane lipoprotein BfpB
Similarity search - Component
Biological speciesEscherichia coli O127:H6 str. E2348/69 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsPei, C.C. / Sun, H. / Yin, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into the secretin complex of a type IVb pilus system.
Authors: Chenchen Pei / Hui Sun / Yinliang Qi / Xiaomei Li / Zhixiong Fang / Manjuan Tang / Rujing Zhang / Zhaofeng Yan / Meng Yin /
Abstract: The bundle-forming pilus (BFP) system in enteropathogenic Escherichia coli (EPEC) produces type IVb pili that enable bacterial auto-aggregation, facilitating bacterial adhesion, colonization, and ...The bundle-forming pilus (BFP) system in enteropathogenic Escherichia coli (EPEC) produces type IVb pili that enable bacterial auto-aggregation, facilitating bacterial adhesion, colonization, and virulence. One of its components, lipoprotein BfpB, interacts with BfpG to form a secretin channel complex that enables pilus translocation across the outer membrane. Here, we report a high-resolution cryo-EM structure of the BfpB-BfpG complex, revealing a 17:17 stoichiometry with stable zigzag-like interactions between BfpG and BfpB near the N3 ring. Secretin BfpB consists of three β-barrels, including an additional N3 barrel that is crucial for BFP biogenesis. As a lipoprotein-type secretin, BfpB possesses an N-terminal LG domain that bridges the N0 domain and the outer membrane, ensuring its correct localization to the bacterial outer membrane. The C-terminal region of the LG domain mediates binding to BfpG, and disruption of these interactions impairs BFP biogenesis. Our results advance our understanding of the assembly mechanism of secretin complexes within the secretin superfamily.
History
DepositionMar 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Nov 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane lipoprotein BfpB
B: Outer membrane lipoprotein BfpB
C: Outer membrane lipoprotein BfpB
D: Outer membrane lipoprotein BfpB
E: Outer membrane lipoprotein BfpB
F: Outer membrane lipoprotein BfpB
G: Outer membrane lipoprotein BfpB
H: Outer membrane lipoprotein BfpB
I: Outer membrane lipoprotein BfpB
J: Outer membrane lipoprotein BfpB
K: Outer membrane lipoprotein BfpB
L: Outer membrane lipoprotein BfpB
M: Outer membrane lipoprotein BfpB
N: Outer membrane lipoprotein BfpB
O: Outer membrane lipoprotein BfpB
P: Outer membrane lipoprotein BfpB
Q: Outer membrane lipoprotein BfpB
R: Lipoprotein
S: Lipoprotein
T: Lipoprotein
U: Lipoprotein
V: Lipoprotein
W: Lipoprotein
X: Lipoprotein
Y: Lipoprotein
Z: Lipoprotein
a: Lipoprotein
b: Lipoprotein
c: Lipoprotein
d: Lipoprotein
e: Lipoprotein
f: Lipoprotein
g: Lipoprotein
h: Lipoprotein


Theoretical massNumber of molelcules
Total (without water)1,175,86534
Polymers1,175,86534
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
Outer membrane lipoprotein BfpB / Bundle-forming pilus B


Mass: 56512.406 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 str. E2348/69 (bacteria)
Gene: bfpB, E2348_P1_005 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47068
#2: Protein
Lipoprotein


Mass: 12656.150 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 str. E2348/69 (bacteria)
Gene: bfpG, E2348_P1_004 / Production host: Escherichia coli (E. coli) / References: UniProt: B7UTD2
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The structure of the BfpBG complex in the T4bP system / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1700 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75445 / Symmetry type: POINT
RefinementHighest resolution: 2.56 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00372913
ELECTRON MICROSCOPYf_angle_d0.49198872
ELECTRON MICROSCOPYf_dihedral_angle_d4.2899945
ELECTRON MICROSCOPYf_chiral_restr0.04311679
ELECTRON MICROSCOPYf_plane_restr0.00412614

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