9PNA | pdb_00009pna

CsgG nanopore in complex with designed CsgX1

• PDB DOI: https://doi.org/10.2210/pdb9PNA/pdb
• EM Map EMD-71748: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): synthetic construct, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-07-19 Released: 2026-09-16 
• Deposition Author(s): Hatstat, A.K., Melo, A., Tse, E., Merz, G.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.61 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

De novo design of semisynthetic conduction pores.

Schnaider, L., Hatstat, A.K., Scott, A.J., Tan, S.K., Hambley, R.G., Dawson, W.M., Griffiths, R.C., Kormos, R.C., Melo, A.A., Tse, E., Polizzi, N.F., Wallace, E.J., Merz, G.E., DeGrado, W.F.

(2026) Nat Struct Mol Biol 

• PubMed: 42768128 
• DOI: https://doi.org/10.1038/s41594-026-01881-w
• Primary Citation Related Structures: 
  9PN8, 9PN9, 9PNA, 9PNB


• PubMed Abstract: 
  

  Protein pores used for molecular sensing are generally assembled from large, multi-subunit natural proteins. Their ion conductance, and thus performance in sensing applications, depends on lumen geometry and chemistry. Here rather than designing a new pore or relying only on mutations to a natural scaffold, we show that installing additional de novo subunits to native protein pore complexes enables large-scale architectural changes. We design de novo proteins that integrate seamlessly with CsgG, a pore widely used in sensing applications, to form 18-subunit, 315-kilodalton semisynthetic conduction pores. This required designing within a confined, nonuniform pore under ninefold symmetry and maintaining an open conducting lumen with a stable, low-noise baseline current. The complexes exhibit distinct current-voltage responses relative to the native pore, including clear rectification, while cryo-electron microscopy confirms the designed lumen architecture, establishing a strategy for modifying existing nano-assemblies with designed protein components under stringent symmetry and structural constraints.

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Organizational Affiliation: 
• Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
Oxford Nanopore Technologies plc, Oxford, UK.
Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA.
Department of Neurology, University of California, San Francisco, CA, USA.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
Oxford Nanopore Technologies plc, Oxford, UK. [e-mail].
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA. [e-mail].
Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA. [e-mail].
Department of Neurology, University of California, San Francisco, CA, USA. [e-mail].
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA. [e-mail].
Cardiovascular Research Institute, University of California, San Francisco, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C9  (Explore in 3D)
Global Stoichiometry: Hetero 18-mer - A9B9 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 325.89 kDa 
• Atom Count: 21,591 
• Modeled Residue Count: 2,790 
• Deposited Residue Count: 2,961 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CsgX1	A, B, C, D, E, F, G, H, I	57	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Curli production assembly/transport component CsgG	J, K, L, M, N, O, P, Q, R	272	Escherichia coli	Mutation(s): 0  Gene Names: csgG, Z1670, ECs1414
UniProt
Find proteins for P0AEA4 (Escherichia coli O157:H7) Explore P0AEA4  Go to UniProtKB:  P0AEA4

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.61 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-16 
Deposition Author(s): Hatstat, A.K., Melo, A., Tse, E., Merz, G.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM147962
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	K99GM155611

Revision History  

• Version 1.0: 2026-09-16
  Type: Initial release
  
• Version 1.1: 2026-10-07
  Changes: Data collection, Database references