6QDW

Cryo-EM structure of the 50S ribosomal subunit at 2.83 Angstroms with modeled GBC SecM peptide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cysteine oxidation and disulfide formation in the ribosomal exit tunnel.

Schulte, L.Mao, J.Reitz, J.Sreeramulu, S.Kudlinzki, D.Hodirnau, V.V.Meier-Credo, J.Saxena, K.Buhr, F.Langer, J.D.Blackledge, M.Frangakis, A.S.Glaubitz, C.Schwalbe, H.

(2020) Nat Commun 11: 5569-5569

  • DOI: https://doi.org/10.1038/s41467-020-19372-x
  • Primary Citation of Related Structures:  
    6QDW

  • PubMed Abstract: 

    Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.


  • Organizational Affiliation

    Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28A [auth 0]78Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29B [auth 1]63Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30C [auth 2]59Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32D [auth 3]57Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33E [auth 4]55Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34F [auth 6]46Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35G [auth 7]65Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36H [auth 8]38Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2K [auth c]273Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3L [auth d]209Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4M [auth e]201Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5N [auth f]179Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6O [auth g]177Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9P [auth h]149Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13Q [auth j]142Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14R [auth k]123Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15S [auth l]144Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16T [auth m]136Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17U [auth n]127Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18V [auth o]117Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19W [auth p]115Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20X [auth q]118Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21Y [auth r]103Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22Z [auth s]110Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23AA [auth t]100Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24BA [auth u]104Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25DA [auth w]94Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27EA [auth y]85Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-crystallin BFA [auth z]61Bos taurusMutation(s): 0 
Gene Names: CRYGB
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Entity ID: 9
MoleculeChains LengthOrganismImage
5S rRNAI [auth a]120Escherichia coli BL21(DE3)
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Entity ID: 10
MoleculeChains LengthOrganismImage
23S rRNAJ [auth b]2,906Escherichia coli BL21(DE3)
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Entity ID: 29
MoleculeChains LengthOrganismImage
glycine-tRNA glyTCA [auth v]75Escherichia coli BL21(DE3)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references