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- EMDB-0842: CsgFG complex with substrate CsgAN6 peptide in Curli biogenesis system -

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Basic information

Entry
Database: EMDB / ID: EMD-0842
TitleCsgFG complex with substrate CsgAN6 peptide in Curli biogenesis system
Map dataCsgFG-CsgAN22
Sample
  • Complex: Curli transport CsgFG complex and substrate CsgAN6 peptide
    • Protein or peptide: Curli production assembly/transport protein CsgG
    • Protein or peptide: CsgF
    • Protein or peptide: Major curlin subunit CsgA
KeywordsBiofilm / Curli biogenesis system / CsgFG Complex / Substrate CsgA / PROTEIN TRANSPORT
Function / homology
Function and homology information


curli secretion complex / curli assembly / protein secretion by the type VIII secretion system / protein transmembrane transport / regulation of amyloid fibril formation / single-species biofilm formation / pilus / cell outer membrane / outer membrane-bounded periplasmic space / amyloid fibril formation ...curli secretion complex / curli assembly / protein secretion by the type VIII secretion system / protein transmembrane transport / regulation of amyloid fibril formation / single-species biofilm formation / pilus / cell outer membrane / outer membrane-bounded periplasmic space / amyloid fibril formation / cell adhesion / identical protein binding / plasma membrane
Similarity search - Function
Curlin associated / Curlin associated repeat / 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 / Major curlin subunit CsgA / Curli production assembly/transport component CsgF / Curli production assembly/transport component CsgF / Curli production assembly/transport component CsgG / Major curlin subunit
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli O69:H11 str. 08-4661 (bacteria) / Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsYan ZF / Yin M
CitationJournal: Nat Commun / Year: 2020
Title: Assembly and substrate recognition of curli biogenesis system.
Authors: Zhaofeng Yan / Meng Yin / Jianan Chen / Xueming Li /
Abstract: A major component of bacterial biofilms is curli amyloid fibrils secreted by the curli biogenesis system. Understanding the curli biogenesis mechanism is critical for developing therapeutic agents ...A major component of bacterial biofilms is curli amyloid fibrils secreted by the curli biogenesis system. Understanding the curli biogenesis mechanism is critical for developing therapeutic agents for biofilm-related infections. Here we report a systematic study of the curli biogenesis system, highlighted by structural, biochemical and functional analysis of the secretion channel complexes (CsgF-CsgG) with and without the curli substrate. The dual-pore architecture of the CsgF-CsgG complex was observed and used to develop an approach to inhibit the curli secretion by physically reducing the size of the CsgF pore. We further elucidated the assembly of the CsgFG complex with curli components (CsgA and CsgB) and curli-cell association through CsgF. Importantly, the recognition of the CsgA substrate by CsgG was uncovered. Nine crevices outside of the CsgG channel provide specific and highly-conserved recognition sites for CsgA N-terminus. Together with analysis of CsgE, our study provides comprehensive insights into curli biogenesis.
History
DepositionNov 1, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 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: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6l7c
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0842.png

Downloads & links

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Map

FileDownload / File: emd_0842.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCsgFG-CsgAN22
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.05
Minimum - Maximum-0.16889569 - 0.34539133
Average (Standard dev.)0.0003715759 (±0.008228281)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.920337.920337.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1690.3450.000

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Supplemental data

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Sample components

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Entire : Curli transport CsgFG complex and substrate CsgAN6 peptide

EntireName: Curli transport CsgFG complex and substrate CsgAN6 peptide
Components
  • Complex: Curli transport CsgFG complex and substrate CsgAN6 peptide
    • Protein or peptide: Curli production assembly/transport protein CsgG
    • Protein or peptide: CsgF
    • Protein or peptide: Major curlin subunit CsgA

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Supramolecule #1: Curli transport CsgFG complex and substrate CsgAN6 peptide

SupramoleculeName: Curli transport CsgFG complex and substrate CsgAN6 peptide
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: Curli production assembly/transport protein CsgG

MacromoleculeName: Curli production assembly/transport protein CsgG / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O69:H11 str. 08-4661 (bacteria)
Molecular weightTheoretical: 30.584035 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

UniProtKB: Curli production assembly/transport component CsgG

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Macromolecule #2: CsgF

MacromoleculeName: CsgF / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.065705 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRVKHAVVLL MLISPLSWAG TMTFQFRNPN FGGNPNNGAF LLNSAQAQNS YKDPSYNDDF GIETPSALDN FTQAIQSQIL GGLLSNINT GKPGRMVTND YIVDIANRDG QLQLNVTDRK TGQTSTIQVS GLQNNSTDF

UniProtKB: Curli production assembly/transport component CsgF

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Macromolecule #3: Major curlin subunit CsgA

MacromoleculeName: Major curlin subunit CsgA / type: protein_or_peptide / ID: 3 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 1.953963 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GVVPQYGGGG NHGGGGNNSG PN

UniProtKB: Major curlin subunit CsgA

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/HE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: OTHER / Details: cylindrical model generated by SPIDER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139702
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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