6QDW image
Entry Detail
PDB ID:
6QDW
EMDB ID:
Keywords:
Title:
Cryo-EM structure of the 50S ribosomal subunit at 2.83 Angstroms with modeled GBC SecM peptide
Biological Source:
PDB Version:
Deposition Date:
2019-01-03
Release Date:
2020-01-15
Method Details:
Experimental Method:
Resolution:
2.83 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:A (auth: 0)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:B (auth: 1)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:C (auth: 2)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:D (auth: 3)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:E (auth: 4)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:F (auth: 6)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:G (auth: 7)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:H (auth: 8)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:I (auth: a)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polyribonucleotide
Description:23S rRNA
Chain IDs:J (auth: b)
Chain Length:2906
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:K (auth: c)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:L (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:M (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:N (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:O (auth: g)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:P (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:Q (auth: j)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:R (auth: k)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:S (auth: l)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:T (auth: m)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:U (auth: n)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:V (auth: o)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:W (auth: p)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:X (auth: q)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:Y (auth: r)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:Z (auth: s)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:AA (auth: t)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:BA (auth: u)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polyribonucleotide
Description:glycine-tRNA glyT
Chain IDs:CA (auth: v)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:DA (auth: w)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:EA (auth: y)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli (strain B / BL21-DE3)
Polymer Type:polypeptide(L)
Description:Gamma-crystallin B
Chain IDs:FA (auth: z)
Chain Length:61
Number of Molecules:1
Biological Source:Bos taurus
Ligand Molecules
Primary Citation
Cysteine oxidation and disulfide formation in the ribosomal exit tunnel.
Nat Commun 11 5569 5569 (2020)
PMID: 33149120 DOI: 10.1038/s41467-020-19372-x

Abstact

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.

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