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: https://doi.org/10.7554/eLife.46267
  • Primary Citation of Related Structures:  
    6R5Q, 6R6G, 6R6P, 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. 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: 1
MoleculeChains Sequence LengthOrganismDetailsImage
eS31A [auth 0]68Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
X-box-binding protein 1B [auth 1]24Homo sapiensMutation(s): 0 
Gene Names: XBP1, TREB5, XBP2
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Find proteins for P17861 (Homo sapiens)
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PHAROS:  P17861
GTEx:  ENSG00000100219 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein RACK1G [auth 6]313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uS14J [auth 9]55Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uL2K [auth A]248Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30L [auth AA]55Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
uL3M [auth B]394Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7N [auth BB]189Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uL4O [auth C]362Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8P [auth CC]206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9 (Predicted)Q [auth DD]185Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5R [auth D]293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S11S [auth EE]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6T [auth E]251Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S28U [auth FF]62Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
uL30V [auth F]225Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S20W [auth GG]100Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
eL8X [auth G]240Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uL6Y [auth H]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21Z [auth HH]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10 (Predicted)AA [auth I]213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
uS13BA [auth II]144Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27CA [auth JJ]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11DA [auth J]170Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eS17FA [auth KK]132Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13GA [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26HA [auth LL]101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L14IA [auth M]138Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14JA [auth MM]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15KA [auth N]203Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24LA [auth NN]124Oryctolagus cuniculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aMA [auth O]199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS25NA [auth OO]75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
uL22OA [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
eS19PA [auth PP]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
eL18QA [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS15RA [auth QQ]149Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19SA [auth R]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12TA [auth RR]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
eL20UA [auth S]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
eS10VA [auth SS]96Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
eL21WA [auth T]159Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15aXA [auth TT]129Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S16YA [auth UU]142Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SGX4 (Oryctolagus cuniculus)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22ZA [auth U]99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S23AB [auth VV]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
eL14BB [auth V]131Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24CB [auth W]121Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
uS19DB [auth WW]120Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
uL23EB [auth X]118Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26FB [auth Y]134Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27GB [auth Z]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
uL15HB [auth a]147Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
eL29IB [auth b]116Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
eL30JB [auth c]98Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
eL31KB [auth d]107Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
eL32LB [auth e]128Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TUN8 (Oryctolagus cuniculus)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
eL33MB [auth f]109Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
eL34NB [auth g]114Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXG5 (Oryctolagus cuniculus)
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
uL29OB [auth h]122Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36PB [auth i]102Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTQ5 (Oryctolagus cuniculus)
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37QB [auth j]86Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38RB [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
eL39SB [auth l]50Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40TB [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60s ribosomal protein l41UB [auth n]25Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
eL42VB [auth o]104Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eL43WB [auth p]91Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
uS2XB [auth q]217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
eL28YB [auth r]124Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0ZB [auth s]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
uL11AC [auth t]153Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aBC [auth u]213Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
uS5CC [auth v]221Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3DC [auth w]228Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4EC [auth x]262Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5FC [auth y]191Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TFM5 (Oryctolagus cuniculus)
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6GC [auth z]237Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TM55 (Oryctolagus cuniculus)
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