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
  • Structures With Same Primary Citation

  • 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: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7BB189Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S11EE151Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
uS13II144Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS18
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
uL4C362Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL4
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
uL30F225Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL7
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L11J170Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
eL22U99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
uL23X118Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100350855
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L26Y134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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Entity ID: 57
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eL29b116Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36i102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL43p91Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100351807LOC100349729RPL37A
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
uS2q217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
uL11t153Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL12
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Entity ID: 85
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uS19WW120Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein Sec61 subunit alpha isoform 1XX461Canis lupus familiarisMutation(s): 0 
Gene Names: SEC61A1
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30AA55Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
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Entity ID: 10
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40S ribosomal protein S27JJ83Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345694LOC100345044LOC100348261RPS27
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
eS17KK132Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353606RPS17
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Entity ID: 12
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eS26LL101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
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uS11MM136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
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eS31068Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
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
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein RACK16313Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
uS14955Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
eS24NN124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS25OO75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
eS19PP141Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345774
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS15QQ149Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12RR117Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
uL2A248Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8CC206Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100352057
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
uL3B394Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5D293Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL5
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6E251Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL6
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
eL8G240Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354898
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
uL6H190Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354760
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L10 (Predicted)I213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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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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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13L210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L14M138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15N203Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL15
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Entity ID: 43
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uL13O199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
uL22P153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
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eL18Q187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
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eL19R180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
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eL20S176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
eL21T159Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
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Entity ID: 50
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eL14V131Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL23
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Entity ID: 51
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Ribosomal protein L24W121Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27Z135Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100356974RPL27
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Entity ID: 55
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eS10SS96Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348511
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Entity ID: 56
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uL15a147Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27ALOC100350771
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Entity ID: 58
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eL30c98Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL30
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Entity ID: 59
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eL31d107Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL31
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S28FF62Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 60
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eL32e128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 61
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eL33f109Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35A
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Entity ID: 62
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eL34g114Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354714
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
uL29h122Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35
Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37j86Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
eL38k69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
eL39l50Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100343258
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
eL40m52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60s ribosomal protein l41n25Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
uS10GG100Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
eL42o104Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353469
Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
eL28r124Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100358162
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0s196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3au213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3ALOC100342838LOC100348981
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
uS5v221Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S3w228Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4x262Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100338112
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
eS21HH83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S5y191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
Find proteins for G1TFM5 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6z237Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S15aTT129Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S16UU142Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS16
Find proteins for G1SGX4 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S23VV141Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS23
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 87
MoleculeChainsSequence LengthOrganismDetails
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
MoleculeChainsSequence LengthOrganismDetails
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: 16
MoleculeChainsLengthOrganism
P-tRNA275Saccharomyces cerevisiae

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Entity ID: 17
MoleculeChainsLengthOrganism
E-tRNA375Saccharomyces cerevisiae
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Entity ID: 18
MoleculeChainsLengthOrganism
messenger RNA46Homo sapiens

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Entity ID: 19
MoleculeChainsLengthOrganism
28S ribosomal RNA53544Oryctolagus cuniculus

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Entity ID: 21
MoleculeChainsLengthOrganism
5S ribosomal RNA7120Oryctolagus cuniculus

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Entity ID: 22
MoleculeChainsLengthOrganism
5.8S ribosomal RNA8151Oryctolagus cuniculus

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Entity ID: 39
MoleculeChainsLengthOrganism
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

Download CCD File 
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