6R7Q

Structure of XBP1u-paused ribosome nascent chain complex with Sec61.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Structural and mutational analysis of the ribosome-arresting human XBP1u.

Shanmuganathan, V.Schiller, N.Magoulopoulou, A.Cheng, J.Braunger, K.Cymer, F.Berninghausen, O.Beatrix, B.Kohno, K.Heijne, G.V.Beckmann, R.

(2019) Elife 8

  • DOI: 10.7554/eLife.46267
  • Primary Citation of Related Structures:  
    6R5Q, 6R6P, 6R6G, 6R7Q

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Gene Center, Department of Biochemistry, Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8CC206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
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Ribosomal protein S9 (Predicted)DD185Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Ribosomal protein S11EE151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
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X-box-binding protein 1124Homo sapiensMutation(s): 0 
Gene Names: XBP1TREB5XBP2
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NIH Common Fund Data Resources
PHAROS  P17861
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Entity ID: 20
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ribosomal protein RACK16313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
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eS19PP141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
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ribosomal protein uS15QQ149Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S12RR117Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L6E251Oryctolagus cuniculusMutation(s): 0 
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uL30F225Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L14M138Oryctolagus cuniculusMutation(s): 0 
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eL19R180Oryctolagus cuniculusMutation(s): 0 
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eL21T159Oryctolagus cuniculusMutation(s): 0 
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eL22U99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
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Ribosomal protein L26Y134Oryctolagus cuniculusMutation(s): 0 
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eS10SS96Oryctolagus cuniculusMutation(s): 0 
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eL29b116Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S4x262Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S30AA55Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S27JJ83Oryctolagus cuniculusMutation(s): 0 
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eS17KK132Oryctolagus cuniculusMutation(s): 0 
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eS26LL101Oryctolagus cuniculusMutation(s): 0 
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uS11MM136Oryctolagus cuniculusMutation(s): 0 
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eS31068Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S7BB189Oryctolagus cuniculusMutation(s): 0 
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uS14955Oryctolagus cuniculusMutation(s): 0 
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eS24NN124Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS25OO75Oryctolagus cuniculusMutation(s): 0 
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uL2A248Oryctolagus cuniculusMutation(s): 0 
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uL3B394Oryctolagus cuniculusMutation(s): 0 
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uL4C362Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L5D293Oryctolagus cuniculusMutation(s): 0 
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eL8G240Oryctolagus cuniculusMutation(s): 0 
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uL6H190Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L10 (Predicted)I213Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L11J170Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L13L210Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L15N203Oryctolagus cuniculusMutation(s): 0 
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uL13O199Oryctolagus cuniculusMutation(s): 0 
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uL22P153Oryctolagus cuniculusMutation(s): 0 
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eL18Q187Oryctolagus cuniculusMutation(s): 0 
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eL20S176Oryctolagus cuniculusMutation(s): 0 
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eL14V131Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L24W121Oryctolagus cuniculusMutation(s): 0 
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uL23X118Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L27Z135Oryctolagus cuniculusMutation(s): 0 
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uL15a147Oryctolagus cuniculusMutation(s): 0 
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eL30c98Oryctolagus cuniculusMutation(s): 0 
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eL31d107Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S28FF62Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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eL32e128Oryctolagus cuniculusMutation(s): 0 
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eL33f109Oryctolagus cuniculusMutation(s): 0 
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eL34g114Oryctolagus cuniculusMutation(s): 0 
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uL29h122Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L36i102Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L37j86Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
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eL39l50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
eL40m52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
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60s ribosomal protein l41n25Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 7
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uS10GG100Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
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eL42o104Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 71
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ribosomal protein eL43p91Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
uS2q217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
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eL28r124Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 74
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60S acidic ribosomal protein P0s196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
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uL11t153Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 76
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40S ribosomal protein S3au213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 77
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uS5v221Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
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Ribosomal protein S3w228Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 8
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eS21HH83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
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Ribosomal protein S5y191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 81
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40S ribosomal protein S6z237Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
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Ribosomal protein S15aTT129Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 83
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Ribosomal protein S16UU142Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
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Ribosomal protein S23VV141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 85
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uS19WW120Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit alpha isoform 1XX461Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61A1
Find proteins for P38377 (Canis lupus familiaris)
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Entity ID: 87
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Protein transport protein Sec61 subunit gammaYY62Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61G
Find proteins for P60058 (Canis lupus familiaris)
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Entity ID: 88
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Protein transport protein Sec61 subunit betaZZ29Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61B
Find proteins for P60467 (Canis lupus familiaris)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
uS13II144Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChainsLengthOrganismImage
E-tRNA375Saccharomyces cerevisiae
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Entity ID: 21
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5S ribosomal RNA7120Oryctolagus cuniculus
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Entity ID: 16
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P-tRNA275Saccharomyces cerevisiae
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  • Entity ID: 18
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    messenger RNA46Homo sapiens
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    Entity ID: 19
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    28S ribosomal RNA53544Oryctolagus cuniculus
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    Entity ID: 22
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    5.8S ribosomal RNA8151Oryctolagus cuniculus
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    Entity ID: 39
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    18S ribosomal RNAK1698Oryctolagus cuniculus
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download CCD File 
    LL, g, j, m, o, p
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    5, 7, 8, B, K, P, V, a, e, g, j, y
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    German Research FoundationGermany--

    Revision History 

    • Version 1.0: 2019-07-10
      Type: Initial release