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- PDB-7brm: Architecture of curli complex -

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Basic information

Entry
Database: PDB / ID: 7brm
TitleArchitecture of curli complex
Components
  • Curli production assembly/transport protein CsgG
  • csgfComputational Science Graduate Fellowship
KeywordsTRANSPORT PROTEIN / curli
Function / homology
Function and homology information


curli secretion complex / curli assembly / protein secretion by the type VIII secretion system / protein transmembrane transport / single-species biofilm formation / cell outer membrane / outer membrane-bounded periplasmic space / identical protein binding / plasma membrane
Similarity search - Function
Type VIII secretion system, CsgF / Type VIII secretion system (T8SS), CsgF protein / Curli production assembly/transport component CsgG / Curli production assembly/transport component CsgG / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Curli production assembly/transport component CsgG / Curli production assembly/transport component CsgF / Curli production assembly/transport component CsgG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhang, M. / Shi, H.
CitationJournal: PLoS Biol / Year: 2020
Title: Cryo-EM structure of the nonameric CsgG-CsgF complex and its implications for controlling curli biogenesis in Enterobacteriaceae.
Authors: Manfeng Zhang / Huigang Shi / Xuemei Zhang / Xinzheng Zhang / Yihua Huang /
Abstract: Curli play critical roles in biofilm formation, host cell adhesion, and colonization of inert surfaces in many Enterobacteriaceae. In Escherichia coli, curli biogenesis requires 7 curli-specific gene ...Curli play critical roles in biofilm formation, host cell adhesion, and colonization of inert surfaces in many Enterobacteriaceae. In Escherichia coli, curli biogenesis requires 7 curli-specific gene (csg) products-CsgA through G-working in concert. Of them, CsgG and CsgF are 2 outer membrane (OM)-localized components that consists of the core apparatus for secretion and assembly of curli structural subunits, CsgB and CsgA. Here, we report the cryogenic electron microscopy (cryo-EM) structure of CsgG in complex with CsgF from E. coli. The structure reveals that CsgF forms a stable complex with CsgG via a 1:1 stoichiometry by lining the upper lumen of the nonameric CsgG channel via its N-terminal 27 residues, forming a funnel-like entity plugged in the CsgG channel and creating a unique secretion channel with 2 constriction regions, consistent with the recently reported structure of the CsgG-CsgF complex. Functional studies indicate that export of CsgF to the cell surface requires the CsgG channel, and CsgF not only functions as an adaptor that bridges CsgB with CsgG but also may play important roles in controlling the rates of translocation and/or polymerization for curli structural subunits. Importantly, we found that a series of CsgF-derived peptides are able to efficiently inhibit curli production to E. coli when administrated exogenously, highlighting a potential strategy to interfere biofilm formation in E. coli strains.
History
DepositionMar 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Curli production assembly/transport protein CsgG
B: Curli production assembly/transport protein CsgG
C: Curli production assembly/transport protein CsgG
D: Curli production assembly/transport protein CsgG
E: Curli production assembly/transport protein CsgG
F: Curli production assembly/transport protein CsgG
G: Curli production assembly/transport protein CsgG
H: Curli production assembly/transport protein CsgG
I: Curli production assembly/transport protein CsgG
a: csgf
b: csgf
c: csgf
d: csgf
e: csgf
f: csgf
g: csgf
h: csgf
i: csgf


Theoretical massNumber of molelcules
Total (without water)410,84818
Polymers410,84818
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area93030 Å2
ΔGint-488 kcal/mol
Surface area83420 Å2

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Components

#1: Protein
Curli production assembly/transport protein CsgG


Mass: 30584.035 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K-12 / Gene: csgG, FAZ83_14740 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V3YU48, UniProt: P0AEA2*PLUS
#2: Protein
csgf / Computational Science Graduate Fellowship


Mass: 15065.705 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AE98*PLUS

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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: curli core complex of CsgG and CsgF / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: YES
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in.
VitrificationCryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 70 K / Residual tilt: 0.1 mradians
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2500
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 3710 / Height: 3838

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 194713
SymmetryPoint symmetry: C9 (9 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115141 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01120646
ELECTRON MICROSCOPYf_angle_d0.78128017
ELECTRON MICROSCOPYf_dihedral_angle_d11.5042835
ELECTRON MICROSCOPYf_chiral_restr0.0483168
ELECTRON MICROSCOPYf_plane_restr0.0043699

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