6R5Q

Structure of XBP1u-paused ribosome nascent chain complex (post-state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
X-box-binding protein 1 124Homo sapiensMutation(s): 0 
Gene Names: XBP1TREB5XBP2
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PHAROS:  P17861
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
uL2 A248Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
uL3 B394Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
uL4 C362Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5 D293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6 E251Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
uL30 F225Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
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eL8 G233Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
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uL6 H190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
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Ribosomal protein L10 (Predicted) I205Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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Entity ID: 16
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Ribosomal protein L11 J170Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
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Entity ID: 17
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60S ribosomal protein L13 L210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
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Ribosomal protein L14 M138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
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Ribosomal protein L15 N203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
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uL13 O199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
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uL22 P153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
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eL18 Q187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
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eL19 R180Oryctolagus cuniculusMutation(s): 0 
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eL20 S176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
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eL21 T159Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
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eL22 U99Oryctolagus cuniculusMutation(s): 0 
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eL14 V131Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
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Ribosomal protein L24 W121Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
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uL23 X118Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
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Ribosomal protein L26 Y134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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Entity ID: 31
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60S ribosomal protein L27 Z135Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27
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Entity ID: 32
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uL15 a147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
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eL29 b104Oryctolagus cuniculusMutation(s): 0 
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eL30 c98Oryctolagus cuniculusMutation(s): 0 
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eL31 d107Oryctolagus cuniculusMutation(s): 0 
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eL32 e128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
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eL33 f109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
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eL34 g114Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
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uL29 h122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
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60S ribosomal protein L36 i102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
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Ribosomal protein L37 j86Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
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eL38 k69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
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eL39 l50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
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eL40 m52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
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60s ribosomal protein l41 n25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
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eL42 o104Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL43 p91Oryctolagus cuniculusMutation(s): 0 
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eL28 r124Oryctolagus cuniculusMutation(s): 0 
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60S acidic ribosomal protein P0 s196Oryctolagus cuniculusMutation(s): 0 
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uL11 t153Oryctolagus cuniculusMutation(s): 0 
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uS2 q217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
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40S ribosomal protein S3a u213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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uS5 v221Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
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Ribosomal protein S3 w228Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 56
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40S ribosomal protein S4 x262Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
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Ribosomal protein S5 y191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 58
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40S ribosomal protein S6 z237Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S7 BB189Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
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40S ribosomal protein S8 CC206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 61
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Ribosomal protein S9 (Predicted) DD185Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Entity ID: 62
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eS10 SS96Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
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Ribosomal protein S11 EE151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
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40S ribosomal protein S12 RR117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 65
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ribosomal protein uS15 QQ149Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS13
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Entity ID: 66
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uS11 MM135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
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uS17 WW120Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
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Entity ID: 68
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Ribosomal protein S16 UU142Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
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eS17 KK132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
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uS13 II144Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
eS19 PP141Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
uS10 GG100Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
eS21 HH83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S15a TT129Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S23 VV141Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 76
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eS24 NN124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eS25 OO75Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 78
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eS26 LL101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
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40S ribosomal protein S27 JJ83Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S28 FF62Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 81
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uS14 955Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 83
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eS31 068Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein RACK1 6313Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 85
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40S ribosomal protein S30 AA55Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 1
MoleculeChainsLengthOrganismImage
E-tRNA375Saccharomyces cerevisiae
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Entity ID: 3
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P-tRNA276Saccharomyces cerevisiae
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Entity ID: 4
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28S ribosomal RNA53543Oryctolagus cuniculus
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Entity ID: 5
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5S rRNA7120Oryctolagus cuniculus
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Entity ID: 6
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5.8S ribosomal RNA8151Oryctolagus cuniculus
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Entity ID: 51
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18S ribosomal RNAK1698Oryctolagus cuniculus
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  • Entity ID: 82
    MoleculeChainsLengthOrganismImage
    mRNA46Homo sapiens
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

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

    Download Ideal Coordinates CCD File 
    5, 7, 8, I, K, P, PP, V, a, e, g, j
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.00 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