6R6G

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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

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 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 ...

    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.



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Entity ID: 1
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eS31A [auth 0]68Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 2
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X-box-binding protein 1B [auth 1]24Homo sapiensMutation(s): 0 
Gene Names: XBP1TREB5XBP2
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ribosomal protein RACK1G [auth 6]313Oryctolagus cuniculusMutation(s): 0 
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uS14J [auth 9]55Oryctolagus cuniculusMutation(s): 0 
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uL2K [auth A]248Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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40S ribosomal protein S30L [auth AA]55Oryctolagus cuniculusMutation(s): 0 
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uL3M [auth B]394Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S7N [auth BB]189Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S8P [auth CC]206Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S9 (Predicted)Q [auth DD]185Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L5R [auth D]293Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L6T [auth E]251Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S28U [auth FF]62Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S21Z [auth HH]83Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L10 (Predicted)AA [auth I]213Oryctolagus cuniculusMutation(s): 0 
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uS13BA [auth II]144Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S27CA [auth JJ]83Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L11DA [auth J]170Oryctolagus cuniculusMutation(s): 0 
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eS17FA [auth KK]132Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L13GA [auth L]210Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S26HA [auth LL]101Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L14IA [auth M]138Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S14JA [auth MM]136Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L15KA [auth N]203Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S24LA [auth NN]124Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L13aMA [auth O]199Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS25NA [auth OO]75Oryctolagus cuniculusMutation(s): 0 
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uL22OA [auth P]153Oryctolagus cuniculusMutation(s): 0 
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eS19PA [auth PP]141Oryctolagus cuniculusMutation(s): 0 
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eL18QA [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS15RA [auth QQ]149Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L19SA [auth R]180Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S12TA [auth RR]117Oryctolagus cuniculusMutation(s): 0 
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eS10VA [auth SS]96Oryctolagus cuniculusMutation(s): 0 
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eL21WA [auth T]159Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S15aXA [auth TT]129Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S16YA [auth UU]142Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L22ZA [auth U]99Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L24CB [auth W]121Oryctolagus cuniculusMutation(s): 0 
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uS19DB [auth WW]120Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L26FB [auth Y]134Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L27GB [auth Z]135Oryctolagus cuniculusMutation(s): 0 
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eL29IB [auth b]116Oryctolagus cuniculusMutation(s): 0 
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eL30JB [auth c]98Oryctolagus cuniculusMutation(s): 0 
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eL32LB [auth e]128Oryctolagus cuniculusMutation(s): 0 
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eL33MB [auth f]109Oryctolagus cuniculusMutation(s): 0 
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eL34NB [auth g]114Oryctolagus cuniculusMutation(s): 0 
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uL29OB [auth h]122Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L36PB [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
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Ribosomal protein L37QB [auth j]86Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
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60S ribosomal protein L38RB [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
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eL39SB [auth l]50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
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60S ribosomal protein L40TB [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
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60s ribosomal protein l41UB [auth n]25Oryctolagus cuniculusMutation(s): 0 
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Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 74
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eL42VB [auth o]104Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 75
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ribosomal protein eL43WB [auth p]91Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 76
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uS2XB [auth q]217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
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eL28YB [auth r]124Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 78
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60S acidic ribosomal protein P0ZB [auth s]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
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uL11AC [auth t]153Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 80
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40S ribosomal protein S3aBC [auth u]213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Entity ID: 81
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uS5CC [auth v]221Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
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Ribosomal protein S3DC [auth w]228Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 83
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40S ribosomal protein S4EC [auth x]262Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 84
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Ribosomal protein S5FC [auth y]191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 85
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40S ribosomal protein S6GC [auth z]237Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 86
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Signal recognition particle 54 kDa proteinHC [auth AB]431Canis lupus familiarisMutation(s): 0 
Gene Names: SRP54
EC: 3.6.5
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Find proteins for P61010 (Canis lupus familiaris)
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Entity ID: 88
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Signal recognition particle subunit SRP19JC [auth AC]105Canis lupus familiarisMutation(s): 0 
Gene Names: SRP19
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Find proteins for J9PAS6 (Canis lupus familiaris)
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Entity ID: 89
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Signal recognition particle subunit SRP68KC [auth AI]195Canis lupus familiarisMutation(s): 0 
Gene Names: SRP68
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Find proteins for Q00004 (Canis lupus familiaris)
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Entity ID: 90
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Signal recognition particle 9 kDa proteinLC [auth AD]74Canis lupus familiarisMutation(s): 0 
Gene Names: SRP9
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Entity ID: 91
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Signal recognition particle 14 kDa proteinMC [auth AE]94Canis lupus familiarisMutation(s): 0 
Gene Names: SRP14
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Find proteins for P16255 (Canis lupus familiaris)
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Entity ID: 92
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Signal sequence (HR2)NC [auth AG]12Homo sapiensMutation(s): 0 
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Entity ID: 3
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P-tRNAC [auth 2]75Saccharomyces cerevisiae
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Entity ID: 4
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E-tRNAD [auth 3]75Saccharomyces cerevisiae
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  • Entity ID: 5
    MoleculeChainsLengthOrganismImage
    mRNAE [auth 4]6Homo sapiens
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    Entity ID: 6
    MoleculeChainsLengthOrganismImage
    28S ribosomal RNAF [auth 5]3544Oryctolagus cuniculus
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    Entity ID: 8
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    5S ribosomal RNAH [auth 7]120Oryctolagus cuniculus
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    Entity ID: 9
    MoleculeChainsLengthOrganismImage
    5.8S ribosomal RNAI [auth 8]151Oryctolagus cuniculus
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    Entity ID: 31
    MoleculeChainsLengthOrganismImage
    18S ribosomal RNAEA [auth K]1698Oryctolagus cuniculus
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    Entity ID: 87
    MoleculeChainsLengthOrganismImage
    7S RNAIC [auth AF]206Canis lupus familiaris
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    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    AO [auth g], BO [auth j], DO [auth m], EO [auth o], FO [auth p]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AD [auth 5] , AE [auth 5] , AF [auth 5] , AG [auth 5] , AH [auth 5] , AI [auth 5] , AJ [auth 5] , AK [auth 5] , 
    AD [auth 5],  AE [auth 5],  AF [auth 5],  AG [auth 5],  AH [auth 5],  AI [auth 5],  AJ [auth 5],  AK [auth 5],  AL [auth K],  AM [auth K],  AN [auth K],  BD [auth 5],  BE [auth 5],  BF [auth 5],  BG [auth 5],  BH [auth 5],  BI [auth 5],  BJ [auth 5],  BK [auth 5],  BL [auth K],  BM [auth K],  BN [auth K],  CD [auth 5],  CE [auth 5],  CF [auth 5],  CG [auth 5],  CH [auth 5],  CI [auth 5],  CJ [auth 5],  CK [auth 5],  CL [auth K],  CM [auth K],  CN [auth K],  CO [auth j],  DD [auth 5],  DE [auth 5],  DF [auth 5],  DG [auth 5],  DH [auth 5],  DI [auth 5],  DJ [auth 5],  DK [auth 5],  DL [auth K],  DM [auth K],  DN [auth K],  ED [auth 5],  EE [auth 5],  EF [auth 5],  EG [auth 5],  EH [auth 5],  EI [auth 5],  EJ [auth 5],  EK [auth 5],  EL [auth K],  EM [auth K],  EN [auth K],  FD [auth 5],  FE [auth 5],  FF [auth 5],  FG [auth 5],  FH [auth 5],  FI [auth 5],  FJ [auth 5],  FK [auth 5],  FL [auth K],  FM [auth K],  FN [auth K],  GD [auth 5],  GE [auth 5],  GF [auth 5],  GG [auth 5],  GH [auth 5],  GI [auth 5],  GJ [auth 5],  GK [auth 5],  GL [auth K],  GM [auth K],  GN [auth K],  HD [auth 5],  HE [auth 5],  HF [auth 5],  HG [auth 5],  HH [auth 5],  HI [auth 5],  HJ [auth 5],  HK [auth 5],  HL [auth K],  HM [auth K],  HN [auth K],  ID [auth 5],  IE [auth 5],  IF [auth 5],  IG [auth 5],  IH [auth 5],  II [auth 5],  IJ [auth 5],  IK [auth 7],  IL [auth K],  IM [auth K],  IN [auth K],  JD [auth 5],  JE [auth 5],  JF [auth 5],  JG [auth 5],  JH [auth 5],  JI [auth 5],  JJ [auth 5],  JK [auth 7],  JL [auth K],  JM [auth K],  JN [auth K],  KD [auth 5],  KE [auth 5],  KF [auth 5],  KG [auth 5],  KH [auth 5],  KI [auth 5],  KJ [auth 5],  KK [auth 7],  KL [auth K],  KM [auth K],  KN [auth K],  LD [auth 5],  LE [auth 5],  LF [auth 5],  LG [auth 5],  LH [auth 5],  LI [auth 5],  LJ [auth 5],  LK [auth 7],  LL [auth K],  LM [auth K],  LN [auth K],  MD [auth 5],  ME [auth 5],  MF [auth 5],  MG [auth 5],  MH [auth 5],  MI [auth 5],  MJ [auth 5],  MK [auth 7],  ML [auth K],  MM [auth K],  MN [auth K],  ND [auth 5],  NE [auth 5],  NF [auth 5],  NG [auth 5],  NH [auth 5],  NI [auth 5],  NJ [auth 5],  NK [auth 7],  NL [auth K],  NM [auth K],  NN [auth K],  OC [auth 5],  OD [auth 5],  OE [auth 5],  OF [auth 5],  OG [auth 5],  OH [auth 5],  OI [auth 5],  OJ [auth 5],  OK [auth 8],  OL [auth K],  OM [auth K],  ON [auth K],  PC [auth 5],  PD [auth 5],  PE [auth 5],  PF [auth 5],  PG [auth 5],  PH [auth 5],  PI [auth 5],  PJ [auth 5],  PK [auth 8],  PL [auth K],  PM [auth K],  PN [auth K],  QC [auth 5],  QD [auth 5],  QE [auth 5],  QF [auth 5],  QG [auth 5],  QH [auth 5],  QI [auth 5],  QJ [auth 5],  QK [auth 8],  QL [auth K],  QM [auth K],  QN [auth K],  RC [auth 5],  RD [auth 5],  RE [auth 5],  RF [auth 5],  RG [auth 5],  RH [auth 5],  RI [auth 5],  RJ [auth 5],  RK [auth 8],  RL [auth K],  RM [auth K],  RN [auth K],  SC [auth 5],  SD [auth 5],  SE [auth 5],  SF [auth 5],  SG [auth 5],  SH [auth 5],  SI [auth 5],  SJ [auth 5],  SK [auth A],  SL [auth K],  SM [auth K],  SN [auth K],  TC [auth 5],  TD [auth 5],  TE [auth 5],  TF [auth 5],  TG [auth 5],  TH [auth 5],  TI [auth 5],  TJ [auth 5],  TK [auth B],  TL [auth K],  TM [auth K],  TN [auth K],  UC [auth 5],  UD [auth 5],  UE [auth 5],  UF [auth 5],  UG [auth 5],  UH [auth 5],  UI [auth 5],  UJ [auth 5],  UK [auth I],  UL [auth K],  UM [auth K],  UN [auth K],  VC [auth 5],  VD [auth 5],  VE [auth 5],  VF [auth 5],  VG [auth 5],  VH [auth 5],  VI [auth 5],  VJ [auth 5],  VK [auth K],  VL [auth K],  VM [auth K],  VN [auth K],  WC [auth 5],  WD [auth 5],  WE [auth 5],  WF [auth 5],  WG [auth 5],  WH [auth 5],  WI [auth 5],  WJ [auth 5],  WK [auth K],  WL [auth K],  WM [auth K],  WN [auth P],  XC [auth 5],  XD [auth 5],  XE [auth 5],  XF [auth 5],  XG [auth 5],  XH [auth 5],  XI [auth 5],  XJ [auth 5],  XK [auth K],  XL [auth K],  XM [auth K],  XN [auth P],  YC [auth 5],  YD [auth 5],  YE [auth 5],  YF [auth 5],  YG [auth 5],  YH [auth 5],  YI [auth 5],  YJ [auth 5],  YK [auth K],  YL [auth K],  YM [auth K],  YN [auth V],  ZC [auth 5],  ZD [auth 5],  ZE [auth 5],  ZF [auth 5],  ZG [auth 5],  ZH [auth 5],  ZI [auth 5],  ZJ [auth 5],  ZK [auth K],  ZL [auth K],  ZM [auth K],  ZN [auth a]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.70 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 FoundationGermanyGRK1721

    Revision History  (Full details and data files)

    • Version 1.0: 2019-07-10
      Type: Initial release
    • Version 1.1: 2019-10-30
      Changes: Advisory, Data collection, Derived calculations