+Open data
-Basic information
Entry | Database: PDB / ID: 6si7 | |||||||||
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Title | Structure of the curli secretion-assembly complex CsgG:CsgF | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / Secretion Channel / Curli / Outer Membrane Protein / Nanopore Sensing / Bacterial amyloid | |||||||||
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 | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Van der Verren, S.E. / Remaut, H. | |||||||||
Funding support | Belgium, 2items
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Citation | Journal: Nat Biotechnol / Year: 2020 Title: A dual-constriction biological nanopore resolves homonucleotide sequences with high fidelity. Authors: Sander E Van der Verren / Nani Van Gerven / Wim Jonckheere / Richard Hambley / Pratik Singh / John Kilgour / Michael Jordan / E Jayne Wallace / Lakmal Jayasinghe / Han Remaut / Abstract: Single-molecule long-read DNA sequencing with biological nanopores is fast and high-throughput but suffers reduced accuracy in homonucleotide stretches. We now combine the CsgG nanopore with the 35- ...Single-molecule long-read DNA sequencing with biological nanopores is fast and high-throughput but suffers reduced accuracy in homonucleotide stretches. We now combine the CsgG nanopore with the 35-residue N-terminal region of its extracellular interaction partner CsgF to produce a dual-constriction pore with improved signal and base-calling accuracy for homopolymer regions. The electron cryo-microscopy structure of CsgG in complex with full-length CsgF shows that the 33 N-terminal residues of CsgF bind inside the β-barrel of the pore, forming a defined second constriction. In complexes of CsgG bound to a 35-residue CsgF constriction peptide, the second constriction is separated from the primary constriction by ~25 Å. We find that both constrictions contribute to electrical signal modulation during single-stranded DNA translocation. DNA sequencing using a prototype CsgG-CsgF protein pore with two constrictions improved single-read accuracy by 25 to 70% in homopolymers up to 9 nucleotides long. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6si7.cif.gz | 434.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6si7.ent.gz | 354.3 KB | Display | PDB format |
PDBx/mmJSON format | 6si7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6si7_validation.pdf.gz | 966.1 KB | Display | wwPDB validaton report |
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Full document | 6si7_full_validation.pdf.gz | 1004.4 KB | Display | |
Data in XML | 6si7_validation.xml.gz | 73.2 KB | Display | |
Data in CIF | 6si7_validation.cif.gz | 97.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/6si7 ftp://data.pdbj.org/pub/pdb/validation_reports/si/6si7 | HTTPS FTP |
-Related structure data
Related structure data | 10206MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 13744.857 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Details: Only first 35 residues were visible and built / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: csgF, b1038, JW1021 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P0AE98 #2: Protein | Mass: 30110.193 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: csgG, b1037, JW1020 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P0AEA2 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CsgG:CsgF complex in DDM / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||
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Molecular weight | Value: 0.40 MDa / Experimental value: NO | ||||||||||||||||
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MC4100 | ||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C43 / Plasmid: pTRC99 | ||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.03 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 56 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2045 |
-Processing
EM software |
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CTF correction | Details: Phase flipping is done internally during relion processing Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C9 (9 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62000 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4UV3 Accession code: 4UV3 / Source name: PDB / Type: experimental model |