7OYA

Cryo-EM structure of the 1 hpf zebrafish embryo 80S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A molecular network of conserved factors keeps ribosomes dormant in the egg.

Leesch, F.Lorenzo-Orts, L.Pribitzer, C.Grishkovskaya, I.Roehsner, J.Chugunova, A.Matzinger, M.Roitinger, E.Belacic, K.Kandolf, S.Lin, T.Y.Mechtler, K.Meinhart, A.Haselbach, D.Pauli, A.

(2023) Nature 613: 712-720

  • DOI: https://doi.org/10.1038/s41586-022-05623-y
  • Primary Citation of Related Structures:  
    7OYA, 7OYB, 7OYC, 7OYD

  • PubMed Abstract: 

    Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed 1-4 . Here, using mass spectrometry and cryo-electron microscopy analyses of ribosomes isolated from zebrafish (Danio rerio) and Xenopus laevis eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four conserved factors that form two modules, consisting of Habp4-eEF2 and death associated protein 1b (Dap1b) or Dap in complex with eIF5a. Both modules occupy functionally important sites and act together to stabilize ribosomes and repress translation. Dap1b (also known as Dapl1 in mammals) is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Addition of recombinant zebrafish Dap1b protein is sufficient to block translation and reconstitute the dormant egg ribosome state in a mammalian translation extract in vitro. Thus, a developmentally programmed, conserved ribosome state has a key role in ribosome storage and translational repression in the egg.


  • Organizational Affiliation

    Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAB [auth A2]308Danio rerioMutation(s): 0 
UniProt
Find proteins for Q803F6 (Danio rerio)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aC [auth B2]267Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6PBY1 (Danio rerio)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2D [auth C2]280Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6NWC3 (Danio rerio)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformE [auth E2]263Danio rerioMutation(s): 0 
UniProt
Find proteins for Q642H9 (Danio rerio)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6F [auth G2]249Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6DHL6 (Danio rerio)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7G [auth H2]194Danio rerioMutation(s): 0 
UniProt
Find proteins for P62084 (Danio rerio)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8H [auth I2]208Danio rerioMutation(s): 0 
UniProt
Find proteins for P62247 (Danio rerio)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9I [auth J2]194Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6P5M3 (Danio rerio)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11J [auth L2]159Danio rerioMutation(s): 0 
UniProt
Find proteins for Q7ZV05 (Danio rerio)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13K [auth N2]151Danio rerioMutation(s): 0 
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Find proteins for Q6IMW6 (Danio rerio)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14L [auth O2]151Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6PBW3 (Danio rerio)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17M [auth R2]134Danio rerioMutation(s): 0 
UniProt
Find proteins for Q5BJA1 (Danio rerio)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21N [auth V2]81Danio rerioMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aO [auth W2]130Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6Q420 (Danio rerio)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23P [auth X2]143Danio rerioMutation(s): 0 
UniProt
Find proteins for A8KB78 (Danio rerio)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24Q [auth Y2]132Danio rerioMutation(s): 0 
UniProt
Find proteins for B7ZD34 (Danio rerio)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26R [auth a2]115Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6P6E2 (Danio rerio)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27S [auth b2]84Danio rerioMutation(s): 0 
UniProt
Find proteins for Q4VBV2 (Danio rerio)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30T [auth e2]133Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6PC01 (Danio rerio)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-(apurinic or apyrimidinic site) lyaseU [auth D2]245Danio rerioMutation(s): 0 
EC: 4.2.99.18
UniProt
Find proteins for Q7ZVD9 (Danio rerio)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5V [auth F2]204Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6PC80 (Danio rerio)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S10W [auth K2]166Danio rerioMutation(s): 0 
UniProt
Find proteins for Q7T1J9 (Danio rerio)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15X [auth P2]145Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6Q421 (Danio rerio)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S16Y [auth Q2]146Danio rerioMutation(s): 0 
UniProt
Find proteins for Q1LWH1 (Danio rerio)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20Z [auth U2]119Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6P6E7 (Danio rerio)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28AA [auth c2]69Danio rerioMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29BA [auth d2]56Danio rerioMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-2-like 1CA [auth g2]317Danio rerioMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25DA [auth Z2]124Danio rerioMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19EA [auth T2]146Danio rerioMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18FA [auth S2]152Danio rerioMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Zgc:103482GA [auth i2]347Danio rerioMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27HA [auth Z1]136Danio rerioMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29IA [auth b1]64Danio rerioMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30JA [auth c1]117Danio rerioMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31KA [auth d1]123Danio rerioMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32LA [auth e1]135Danio rerioMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aMA [auth f1]110Danio rerioMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34NA [auth g1]117Danio rerioMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35OA [auth h1]123Danio rerioMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36PA [auth i1]105Danio rerioMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37QA [auth j1]97Danio rerioMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38RA [auth k1]70Danio rerioMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aSA [auth o1]106Danio rerioMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Zgc:171772TA [auth p1]92Danio rerioMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8UA [auth A1]257Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6P0V6 (Danio rerio)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3VA [auth B1]403Danio rerioMutation(s): 0 
UniProt
Find proteins for A0A2R8Q924 (Danio rerio)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L4WA [auth C1]375Danio rerioMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L5bXA [auth D1]296Danio rerioMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6YA [auth E1]265Danio rerioMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L7ZA [auth F1]246Danio rerioMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aAB [auth G1]266Danio rerioMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9BB [auth H1]192Danio rerioMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11CB [auth J1]178Danio rerioMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13DB [auth L1]211Danio rerioMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14EB [auth M1]139Danio rerioMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15FB [auth N1]204Danio rerioMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aGB [auth O1]205Danio rerioMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17HB [auth P1]184Danio rerioMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18IB [auth Q1]182Danio rerioMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19JB [auth R1]196Danio rerioMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21KB [auth T1]160Danio rerioMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L22LB [auth U1]141Danio rerioMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23MB [auth V1]140Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6PC14 (Danio rerio)
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24NB [auth W1]157Danio rerioMutation(s): 0 
UniProt
Find proteins for A0A0R4IMS3 (Danio rerio)
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23aOB [auth X1]155Danio rerioMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase H+ transporting V0 subunit e1PB [auth Y1]145Danio rerioMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L39QB [auth l1]51Danio rerioMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41RB [auth n1]25Danio rerioMutation(s): 0 
UniProt
Find proteins for A0A0R4ILF4 (Danio rerio)
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28SB [auth r1]138Danio rerioMutation(s): 0 
UniProt
Find proteins for F1QFV6 (Danio rerio)
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10TB [auth I1]215Danio rerioMutation(s): 0 
UniProt
Find proteins for Q7ZV96 (Danio rerio)
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aUB [auth S1]176Danio rerioMutation(s): 0 
UniProt
Find proteins for Q7ZWJ4 (Danio rerio)
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40VB [auth m1]128Danio rerioMutation(s): 0 
UniProt
Find proteins for Q3B7P7 (Danio rerio)
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aWB [auth a1]148Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6P2M0 (Danio rerio)
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Novel protein similar to human proliferation-associated 2G4 protein (PA2G4)AC [auth q1]392Danio rerioMutation(s): 0 
UniProt
Find proteins for Q8AW82 (Danio rerio)
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