3J9M

Structure of the human mitochondrial ribosome (class 1)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Ribosome. The structure of the human mitochondrial ribosome.

Amunts, A., Brown, A., Toots, J., Scheres, S.H., Ramakrishnan, V.

(2015) Science 348: 95-98

  • DOI: https://doi.org/10.1126/science.aaa1193
  • Primary Citation of Related Structures:  
    3J9M

  • PubMed Abstract: 

    The highly divergent ribosomes of human mitochondria (mitoribosomes) synthesize 13 essential proteins of oxidative phosphorylation complexes. We have determined the structure of the intact mitoribosome to 3.5 angstrom resolution by means of single-particle electron cryogenic microscopy. It reveals 80 extensively interconnected proteins, 36 of which are specific to mitochondria, and three ribosomal RNA molecules. The head domain of the small subunit, particularly the messenger (mRNA) channel, is highly remodeled. Many intersubunit bridges are specific to the mitoribosome, which adopts conformations involving ratcheting or rolling of the small subunit that are distinct from those seen in bacteria or eukaryotes. An intrinsic guanosine triphosphatase mediates a contact between the head and central protuberance. The structure provides a reference for analysis of mutations that cause severe pathologies and for future drug design.

    • Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uL2mC [auth D]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112651 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uL3mD [auth E]348Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114686 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uL4mE [auth F]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105364 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
bL9mF [auth H]267Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143436 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uL10mG [auth I]261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159111 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uL11mH [auth J]192Homo sapiensMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uL13mI [auth K]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172172 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL14mJ [auth L]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180992 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uL15mK [auth M]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137547 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
uL16mL [auth N]251Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166902 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
bL17mM [auth O]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000158042 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL18mN [auth P]179Homo sapiensMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
bL19mO [auth Q]292Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115364 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
bL20mP [auth R]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242485 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
bL21mQ [auth S]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197345 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uL22mR [auth T]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082515 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uL23mS [auth U]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000214026 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uL24mT [auth V]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143314 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
bL27mU [auth W]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108826 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
bL28mV [auth X]256Homo sapiensMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
uL29mW [auth Y]250Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136522 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uL30mX [auth Z]161Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185414 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
bL32mY [auth 0]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106591 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
bL33mZ [auth 1]65Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243147 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
bL34mAA [auth 2]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130312 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
bL35mBA [auth 3]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132313 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
bL36mCA [auth 4]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171421 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
mL37DA [auth 5]423Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116221 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
mL38EA [auth 6]380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204316 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
mL39FA [auth 7]338Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000154719 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
mL40GA [auth 8]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185608 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
mL41HA [auth 9]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182154 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
mL42IA [auth a]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198015 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
mL43JA [auth b]155Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000055950 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
mL44KA [auth c]332Homo sapiensMutation(s): 0 
EC: 3.1.26
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GTEx:  ENSG00000135900 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
mL45LA [auth d]306Homo sapiensMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
mL46MA [auth e]279Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000259494 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
mL48NA [auth f]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175581 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
mL49OA [auth g]166Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149792 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
mL50PA [auth h]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136897 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
mL51QA [auth i]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111639 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
mL52RA [auth j]123Homo sapiensMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
mL53SA [auth k]112Homo sapiensMutation(s): 0 
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Find proteins for Q96EL3 (Homo sapiens)
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GTEx:  ENSG00000204822 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
mL54TA [auth l]138Homo sapiensMutation(s): 0 
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Find proteins for Q6P161 (Homo sapiens)
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GTEx:  ENSG00000183617 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
bL31mUA [auth m]128Homo sapiensMutation(s): 0 
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Find proteins for Q7Z7F7 (Homo sapiens)
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GTEx:  ENSG00000162910 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
mL63VA [auth o]102Homo sapiensMutation(s): 0 
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Find proteins for Q9BQC6 (Homo sapiens)
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GTEx:  ENSG00000173141 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
mL62 (ICT1)WA [auth p]206Homo sapiensMutation(s): 0 
EC: 3.1.1.29
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Find proteins for Q14197 (Homo sapiens)
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GTEx:  ENSG00000167862 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
mL64 (CRIF1)XA [auth q]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000179271 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
mL66 (bS18a)YA [auth r]196Homo sapiensMutation(s): 0 
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Find proteins for Q9NVS2 (Homo sapiens)
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GTEx:  ENSG00000096080 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
mL65 (mS30)ZA [auth s]439Homo sapiensMutation(s): 0 
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Find proteins for Q9NP92 (Homo sapiens)
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GTEx:  ENSG00000112996 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein/protein extensionAB [auth t]28Homo sapiensMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
uS2mDB [auth AB]296Homo sapiensMutation(s): 0 
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Find proteins for Q9Y399 (Homo sapiens)
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GTEx:  ENSG00000122140 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
uS3mEB [auth AC]167Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000062582 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
uS5mFB [auth AD]430Homo sapiensMutation(s): 0 
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Find proteins for P82675 (Homo sapiens)
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GTEx:  ENSG00000144029 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
bS6mGB [auth AE]125Homo sapiensMutation(s): 0 
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Find proteins for P82932 (Homo sapiens)
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GTEx:  ENSG00000243927 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
uS7mHB [auth AF]242Homo sapiensMutation(s): 0 
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Find proteins for Q9Y2R9 (Homo sapiens)
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GTEx:  ENSG00000125445 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
uS9mIB [auth AG]396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135972 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
uS10mJB [auth AH]201Homo sapiensMutation(s): 0 
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Find proteins for P82664 (Homo sapiens)
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GTEx:  ENSG00000048544 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
uS11mKB [auth AI]194Homo sapiensMutation(s): 0 
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Find proteins for P82912 (Homo sapiens)
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GTEx:  ENSG00000181991 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
uS12mLB [auth AJ]138Homo sapiensMutation(s): 0 
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Find proteins for O15235 (Homo sapiens)
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GTEx:  ENSG00000128626 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
uS14mMB [auth AK]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120333 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
uS15mNB [auth AL]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116898 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
bS16mOB [auth AM]137Homo sapiensMutation(s): 0 
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Find proteins for Q9Y3D3 (Homo sapiens)
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GTEx:  ENSG00000182180 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
uS17mPB [auth AN]130Homo sapiensMutation(s): 0 
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Find proteins for Q9Y2R5 (Homo sapiens)
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GTEx:  ENSG00000239789 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
mS40 (bS18b)QB [auth AO]258Homo sapiensMutation(s): 0 
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Find proteins for Q9Y676 (Homo sapiens)
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GTEx:  ENSG00000204568 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
bS18m (bS18c)RB [auth AP]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163319 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
bS21mSB [auth AQ]87Homo sapiensMutation(s): 0 
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Find proteins for P82921 (Homo sapiens)
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GTEx:  ENSG00000266472 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
mS22TB [auth AR]360Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175110 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
mS23UB [auth AS]190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181610 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
mS25VB [auth AT]173Homo sapiensMutation(s): 0 
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