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- PDB-9pna: CsgG nanopore in complex with designed CsgX1 -

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Basic information

Entry
Database: PDB / ID: 9pna
TitleCsgG nanopore in complex with designed CsgX1
Components
  • CsgX1
  • Curli production assembly/transport component CsgG
KeywordsMEMBRANE PROTEIN / complex / de novo design / nanopore
Function / homologyCurli production assembly/transport component CsgG / Curli production assembly/transport component CsgG / outer membrane-bounded periplasmic space / Prokaryotic membrane lipoprotein lipid attachment site profile. / identical protein binding / plasma membrane / Curli production assembly/transport component CsgG
Function and homology information
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsHatstat, A.K. / Melo, A. / Tse, E. / Merz, G.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM147962 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM155611 United States
CitationJournal: To Be Published
Title: De novo design of semisynthetic protein nanopores
Authors: Schnaider, L.S. / Hatstat, A.K. / Scott, A.J. / Tan, S. / Hambley, R. / Dawson, W. / Polizzi, N. / Wallace, E.J. / Merz, G.E. / DeGrado, W.F.
History
DepositionJul 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CsgX1
B: CsgX1
C: CsgX1
D: CsgX1
E: CsgX1
F: CsgX1
G: CsgX1
H: CsgX1
I: CsgX1
J: Curli production assembly/transport component CsgG
K: Curli production assembly/transport component CsgG
L: Curli production assembly/transport component CsgG
M: Curli production assembly/transport component CsgG
N: Curli production assembly/transport component CsgG
O: Curli production assembly/transport component CsgG
P: Curli production assembly/transport component CsgG
Q: Curli production assembly/transport component CsgG
R: Curli production assembly/transport component CsgG


Theoretical massNumber of molelcules
Total (without water)325,88918
Polymers325,88918
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
CsgX1


Mass: 6118.722 Da / Num. of mol.: 9 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein
Curli production assembly/transport component CsgG


Mass: 30091.146 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: csgG, Z1670, ECs1414 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEA4
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: Nanopore assembly of CsgG nonamer with CsgX1C nonamer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 46 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C9 (9 fold cyclic)
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79368 / Symmetry type: POINT

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