5A7U | pdb_00005a7u

Single-particle cryo-EM of co-translational folded adr1 domain inside the E. coli ribosome exit tunnel.

• PDB DOI: https://doi.org/10.2210/pdb5A7U/pdb
• EM Map EMD-3079: EMDB EMDataResource

• Classification: TRANSLATION
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-10 Released: 2015-09-16 
• Deposition Author(s): Nilsson, O.B., Hedman, R., Marino, J., Wickles, S., Bischoff, L., Johansson, M., Muller-Lucks, A., Trovato, F., Puglisi, J.D., O'Brien, E., Beckmann, R., von Heijne, G.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cotranslational Protein Folding Inside the Ribosome Exit Tunnel.

Nilsson, O.B., Hedman, R., Marino, J., Wickles, S., Bischoff, L., Johansson, M., Muller-Lucks, A., Trovato, F., Puglisi, J.D., O'Brien, E.P., Beckmann, R., Von Heijne, G.

(2015) Cell Rep 12: 1533

• PubMed: 26321634 
• DOI: https://doi.org/10.1016/j.celrep.2015.07.065
• Primary Citation Related Structures: 
  5A7U


• PubMed Abstract: 
  

  At what point during translation do proteins fold? It is well established that proteins can fold cotranslationally outside the ribosome exit tunnel, whereas studies of folding inside the exit tunnel have so far detected only the formation of helical secondary structure and collapsed or partially structured folding intermediates. Here, using a combination of cotranslational nascent chain force measurements, inter-subunit fluorescence resonance energy transfer studies on single translating ribosomes, molecular dynamics simulations, and cryoelectron microscopy, we show that a small zinc-finger domain protein can fold deep inside the vestibule of the ribosome exit tunnel. Thus, for small protein domains, the ribosome itself can provide the kind of sheltered folding environment that chaperones provide for larger proteins.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91 Stockholm, Sweden.
Gene Center and Center for Integrated Protein Science Munich, CiPS-M, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany.
Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, 751 24 Uppsala, Sweden.
Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA; Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91 Stockholm, Sweden; Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 3.47 kDa 
• Atom Count: 224 
• Modeled Residue Count: 27 
• Deposited Residue Count: 29 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REGULATORY PROTEIN ADR1	A	29	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P07248 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07248  Go to UniProtKB:  P07248

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPIDER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Nilsson, O.B., Hedman, R., Marino, J., Wickles, S., Bischoff, L., Johansson, M., Muller-Lucks, A., Trovato, F., Puglisi, J.D., O'Brien, E., Beckmann, R., von Heijne, G.

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 1.1: 2015-09-23
  Changes: Database references
• Version 1.2: 2017-08-23
  Changes: Data collection
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Refinement description