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- EMDB-0945: High resolution architecture of curli complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0945
TitleHigh resolution architecture of curli complex
Map data
Sample
  • Complex: curli core complex of CsgG and CsgF
    • Protein or peptide: Curli production assembly/transport component CsgG
    • Protein or peptide: Curli production assembly/transport component CsgF
Keywordscurli / TRANSPORT PROTEIN
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 CsgF / Curli production assembly/transport component CsgG
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 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
DepositionJan 13, 2020-
Header (metadata) releaseJul 15, 2020-
Map releaseJul 15, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lqh
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6lqh
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0945.png

Downloads & links

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Map

FileDownload / File: emd_0945.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.025
Minimum - Maximum-0.083353244 - 0.14044715
Average (Standard dev.)0.0005916429 (±0.0059305197)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0830.1400.001

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Supplemental data

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Half map: #2

Fileemd_0945_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_0945_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : curli core complex of CsgG and CsgF

EntireName: curli core complex of CsgG and CsgF
Components
  • Complex: curli core complex of CsgG and CsgF
    • Protein or peptide: Curli production assembly/transport component CsgG
    • Protein or peptide: Curli production assembly/transport component CsgF

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Supramolecule #1: curli core complex of CsgG and CsgF

SupramoleculeName: curli core complex of CsgG and CsgF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12

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Macromolecule #1: Curli production assembly/transport component CsgG

MacromoleculeName: Curli production assembly/transport component CsgG / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 31.62618 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQRLFLLVAV MLLSGCLTAP PKEAARPTLM PRAQSYKDLT HLPAPTGKIF VSVYNIQDET GQFKPYPASN FSTAVPQSAT AMLVTALKD SRWFIPLERQ GLQNLLNERK IIRAAQENGT VAINNRIPLQ SLTAANIMVE GSIIGYESNV KSGGVGARYF G IGADTQYQ ...String:
MQRLFLLVAV MLLSGCLTAP PKEAARPTLM PRAQSYKDLT HLPAPTGKIF VSVYNIQDET GQFKPYPASN FSTAVPQSAT AMLVTALKD SRWFIPLERQ GLQNLLNERK IIRAAQENGT VAINNRIPLQ SLTAANIMVE GSIIGYESNV KSGGVGARYF G IGADTQYQ LDQIAVNLRV VNVSTGEILS SVNTSKTILS YEVQAGVFRF IDYQRLLEGE VGYTSNEPVM LCLMSAIETG VI FLINDGI DRGLWDLQNK AERQNDILVK YRHMSVPPES WSHPQFEK

UniProtKB: Curli production assembly/transport component CsgG

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Macromolecule #2: Curli production assembly/transport component CsgF

MacromoleculeName: Curli production assembly/transport component CsgF / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 15.894586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRVKHAVVLL MLISPLSWAG TMTFQFRNPN FGGNPNNGAF LLNSAQAQNS YKDPSYNDDF GIETPSALDN FTQAIQSQIL GGLLSNINT GKPGRMVTND YIVDIANRDG QLQLNVTDRK TGQTSTIQVS GLQNNSTDFH HHHHH

UniProtKB: Curli production assembly/transport component CsgF

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridMaterial: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
TemperatureMin: 70.0 K
Alignment procedureComa free - Residual tilt: 0.1 mrad
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 2500 / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 265188
Startup modelType of model: PDB ENTRY
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D9 (2x9 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 101241
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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