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Structure paper

TitleStructural and mutational analysis of the ribosome-arresting human XBP1u.
Journal, issue, pagesElife, Vol. 8, Year 2019
Publish dateJun 27, 2019
AuthorsVivekanandan Shanmuganathan / Nina Schiller / Anastasia Magoulopoulou / Jingdong Cheng / Katharina Braunger / Florian Cymer / Otto Berninghausen / Birgitta Beatrix / Kenji Kohno / Gunnar von Heijne / Roland Beckmann /
PubMed AbstractXBP1u, a central component of the unfolded protein response (UPR), is a mammalian protein containing a functionally critical translational arrest peptide (AP). Here, we present a 3 Å cryo-EM ...XBP1u, a central component of the unfolded protein response (UPR), is a mammalian protein containing a functionally critical translational arrest peptide (AP). Here, we present a 3 Å cryo-EM structure of the stalled human XBP1u AP. It forms a unique turn in the ribosomal exit tunnel proximal to the peptidyl transferase center where it causes a subtle distortion, thereby explaining the temporary translational arrest induced by XBP1u. During ribosomal pausing the hydrophobic region 2 (HR2) of XBP1u is recognized by SRP, but fails to efficiently gate the Sec61 translocon. An exhaustive mutagenesis scan of the XBP1u AP revealed that only 8 out of 20 mutagenized positions are optimal; in the remaining 12 positions, we identify 55 different mutations increase the level of translational arrest. Thus, the wildtype XBP1u AP induces only an intermediate level of translational arrest, allowing efficient targeting by SRP without activating the Sec61 channel.
External linksElife / PubMed:31246176 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 3.9 Å
Structure data

4729

6r5q

EMDB-4729, PDB-6r5q:
Structure of XBP1u-paused ribosome nascent chain complex (post-state)
Method: EM (single particle) / Resolution: 3.0 Å

4735

6r6g

EMDB-4735, PDB-6r6g:
Structure of XBP1u-paused ribosome nascent chain complex with SRP.
Method: EM (single particle) / Resolution: 3.7 Å

4737

6r6p

EMDB-4737, PDB-6r6p:
Structure of XBP1u-paused ribosome nascent chain complex (rotated state)
Method: EM (single particle) / Resolution: 3.1 Å

4745

6r7q

EMDB-4745, PDB-6r7q:
Structure of XBP1u-paused ribosome nascent chain complex with Sec61.
Method: EM (single particle) / Resolution: 3.9 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

Source
  • oryctolagus cuniculus (rabbit)
  • saccharomyces cerevisiae (brewer's yeast)
  • homo sapiens (human)
  • Rabbit (rabbit)
  • canis lupus familiaris (dog)
  • Dog (dog)
  • Human (human)
  • Baker's yeast (brewer's yeast)
KeywordsRIBOSOME / translational pausing / XBP1 / UPR / cotranslational targeting / SRP.

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