8PXS | pdb_00008pxs

Short RNA binding to peptide amyloids

• PDB DOI: https://doi.org/10.2210/pdb8PXS/pdb
• NAKB: 8PXS
• BMRB: 34838

• Classification: UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-24 Released: 2023-10-18 
• Deposition Author(s): Rout, S.K., Cadalbert, R., Schroder, N., Wiegand, T., Zehnder, J., Gampp, O., Guntert, P., Kringler, D., Kreutz, C., Knorlein, A., Hall, J., Greenwald, J., Riek, R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Calculated: 4000 
• Conformers Submitted: 10 
• Selection Criteria: target function 

Literature

An Analysis of Nucleotide-Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA.

Rout, S.K., Cadalbert, R., Schroder, N., Wang, J., Zehnder, J., Gampp, O., Wiegand, T., Guntert, P., Klingler, D., Kreutz, C., Knorlein, A., Hall, J., Greenwald, J., Riek, R.

(2023) J Am Chem Soc 145: 21915-21924

• PubMed: 37782045 
• DOI: https://doi.org/10.1021/jacs.3c06287
• Primary Citation Related Structures: 
  8PXS


• PubMed Abstract: 
  

  Interactions between RNA and proteins are the cornerstone of many important biological processes from transcription and translation to gene regulation, yet little is known about the ancient origin of said interactions. We hypothesized that peptide amyloids played a role in the origin of life and that their repetitive structure lends itself to building interfaces with other polymers through avidity. Here, we report that short RNA with a minimum length of three nucleotides binds in a sequence-dependent manner to peptide amyloids. The 3'-5' linked RNA backbone appears to be well-suited to support these interactions, with the phosphodiester backbone and nucleobases both contributing to the affinity. Sequence-specific RNA-peptide interactions of the kind identified here may provide a path to understanding one of the great mysteries rooted in the origin of life: the origin of the genetic code.

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Organizational Affiliation: 
• Institute of Molecular Physical Science, ETH Zürich, 8093 Zürich, Switzerland.
Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany.
Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim/Ruhr, Germany.
Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany.
Department of Chemistry, Tokyo Metropolitan University, Hachioji 192-0397, Japan.
Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, 6020 Innsbruck, Austria.
Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 9.78 kDa 
• Atom Count: 685 
• Modeled Residue Count: 94 
• Deposited Residue Count: 94 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	A, B, C, E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J]	9	Escherichia coli	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*UP*CP*A)-3')	D [auth R]	4	Escherichia coli

Experimental Data & Validation

Experimental Data

• Method: SOLID-STATE NMR
• Conformers Calculated: 4000 
• Conformers Submitted: 10 
• Selection Criteria: target function 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Rout, S.K., Cadalbert, R., Schroder, N., Wiegand, T., Zehnder, J., Gampp, O., Guntert, P., Kringler, D., Kreutz, C., Knorlein, A., Hall, J., Greenwald, J., Riek, R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Database references, Structure summary