7OYB

Cryo-EM structure of the 6 hpf zebrafish embryo 80S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8E [auth A1]257Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6P0V6 (Danio rerio)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAF [auth A2]308Danio rerioMutation(s): 0 
UniProt
Find proteins for Q803F6 (Danio rerio)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3G [auth B1]403Danio rerioMutation(s): 0 
UniProt
Find proteins for A0A2R8Q924 (Danio rerio)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aH [auth B2]267Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6PBY1 (Danio rerio)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L4I [auth C1]375Danio rerioMutation(s): 0 
UniProt
Find proteins for Q7ZW95 (Danio rerio)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2J [auth C2]280Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6NWC3 (Danio rerio)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L5bK [auth D1]296Danio rerioMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-(apurinic or apyrimidinic site) lyaseL [auth D2]245Danio rerioMutation(s): 0 
EC: 4.2.99.18
UniProt
Find proteins for Q7ZVD9 (Danio rerio)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6M [auth E1]265Danio rerioMutation(s): 0 
UniProt
Find proteins for Q567N5 (Danio rerio)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformN [auth E2]263Danio rerioMutation(s): 0 
UniProt
Find proteins for Q642H9 (Danio rerio)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L7O [auth F1]246Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6Q417 (Danio rerio)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5P [auth F2]204Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6PC80 (Danio rerio)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aQ [auth G1]266Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6PBZ1 (Danio rerio)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6R [auth G2]249Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6DHL6 (Danio rerio)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9S [auth H1]192Danio rerioMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7T [auth H2]194Danio rerioMutation(s): 0 
UniProt
Find proteins for P62084 (Danio rerio)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10U [auth I1]215Danio rerioMutation(s): 0 
UniProt
Find proteins for Q7ZV96 (Danio rerio)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8V [auth I2]208Danio rerioMutation(s): 0 
UniProt
Find proteins for P62247 (Danio rerio)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11W [auth J1]178Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6IQI6 (Danio rerio)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9X [auth J2]194Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6P5M3 (Danio rerio)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S10Y [auth K2]166Danio rerioMutation(s): 0 
UniProt
Find proteins for Q7T1J9 (Danio rerio)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13Z [auth L1]211Danio rerioMutation(s): 0 
UniProt
Find proteins for Q90Z10 (Danio rerio)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11AA [auth L2]159Danio rerioMutation(s): 0 
UniProt
Find proteins for Q7ZV05 (Danio rerio)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14BA [auth M1]139Danio rerioMutation(s): 0 
UniProt
Find proteins for A8E526 (Danio rerio)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15CA [auth N1]204Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6DHS3 (Danio rerio)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13DA [auth N2]151Danio rerioMutation(s): 0 
UniProt
Find proteins for Q6IMW6 (Danio rerio)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aEA [auth O1]205Danio rerioMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14FA [auth O2]151Danio rerioMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17GA [auth P1]184Danio rerioMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15HA [auth P2]145Danio rerioMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18IA [auth Q1]182Danio rerioMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S16JA [auth Q2]146Danio rerioMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19KA [auth R1]196Danio rerioMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17LA [auth R2]134Danio rerioMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aMA [auth S1]176Danio rerioMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18NA [auth S2]152Danio rerioMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21OA [auth T1]160Danio rerioMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19PA [auth T2]146Danio rerioMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L22QA [auth U1]141Danio rerioMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20RA [auth U2]119Danio rerioMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23SA [auth V1]140Danio rerioMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21TA [auth V2]81Danio rerioMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24UA [auth W1]157Danio rerioMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aVA [auth W2]130Danio rerioMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23aWA [auth X1]155Danio rerioMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23XA [auth X2]143Danio rerioMutation(s): 0 
UniProt
Find proteins for A8KB78 (Danio rerio)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase H+ transporting V0 subunit e1YA [auth Y1]145Danio rerioMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24ZA [auth Y2]132Danio rerioMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27AB [auth Z1]136Danio rerioMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25BB [auth Z2]124Danio rerioMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aCB [auth a1]148Danio rerioMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26DB [auth a2]115Danio rerioMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29EB [auth b1]64Danio rerioMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27FB [auth b2]84Danio rerioMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30GB [auth c1]117Danio rerioMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28HB [auth c2]69Danio rerioMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31IB [auth d1]123Danio rerioMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29JB [auth d2]56Danio rerioMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32KB [auth e1]135Danio rerioMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30LB [auth e2]133Danio rerioMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aMB [auth f1]110Danio rerioMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34NB [auth g1]117Danio rerioMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-2-like 1OB [auth g2]317Danio rerioMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35PB [auth h1]123Danio rerioMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36QB [auth i1]105Danio rerioMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37RB [auth j1]97Danio rerioMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38SB [auth k1]70Danio rerioMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L39TB [auth l1]50Danio rerioMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40UB [auth m1]128Danio rerioMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Rpl41VB [auth n1]25Danio rerioMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aWB [auth o1]106Danio rerioMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Zgc:171772XB [auth p1]92Danio rerioMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28YB [auth r1]138Danio rerioMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth 22]1,939Danio rerio
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Entity ID: 2
MoleculeChains LengthOrganismImage
28S rRNAB [auth 51]4,269Danio rerio
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth 71]120Danio rerio
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Entity ID: 4
MoleculeChains LengthOrganismImage
5.8S rRNAD [auth 81]158Danio rerio
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AK [auth p1]
RJ [auth a2]
TJ [auth d2]
VJ [auth g1]
WJ [auth j1]
AK [auth p1],
RJ [auth a2],
TJ [auth d2],
VJ [auth g1],
WJ [auth j1],
YJ [auth m1],
ZJ [auth o1]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth 51]
AD [auth 51]
AE [auth 51]
AF [auth 51]
AG [auth 51]
AC [auth 51],
AD [auth 51],
AE [auth 51],
AF [auth 51],
AG [auth 51],
AH [auth 51],
AI [auth 51],
AJ [auth 51],
BC [auth 51],
BD [auth 51],
BE [auth 51],
BF [auth 51],
BG [auth 51],
BH [auth 51],
BI [auth 51],
BJ [auth 51],
CC [auth 51],
CD [auth 51],
CE [auth 51],
CF [auth 51],
CG [auth 51],
CH [auth 51],
CI [auth 51],
CJ [auth 51],
DC [auth 51],
DD [auth 51],
DE [auth 51],
DF [auth 51],
DG [auth 51],
DH [auth 51],
DI [auth 51],
DJ [auth 51],
EC [auth 51],
ED [auth 51],
EE [auth 51],
EF [auth 51],
EG [auth 51],
EH [auth 51],
EI [auth 51],
EJ [auth 51],
FC [auth 51],
FD [auth 51],
FE [auth 51],
FF [auth 51],
FG [auth 51],
FH [auth 51],
FI [auth 51],
FJ [auth 51],
GC [auth 51],
GD [auth 51],
GE [auth 51],
GF [auth 51],
GG [auth 51],
GH [auth 51],
GI [auth 51],
GJ [auth 71],
HC [auth 51],
HD [auth 51],
HE [auth 51],
HF [auth 51],
HG [auth 51],
HH [auth 51],
HI [auth 51],
HJ [auth 71],
IC [auth 51],
ID [auth 51],
IE [auth 51],
IF [auth 51],
IG [auth 51],
IH [auth 51],
II [auth 51],
IJ [auth 71],
JC [auth 51],
JD [auth 51],
JE [auth 51],
JF [auth 51],
JG [auth 51],
JH [auth 51],
JI [auth 51],
JJ [auth 81],
KC [auth 51],
KD [auth 51],
KE [auth 51],
KF [auth 51],
KG [auth 51],
KH [auth 51],
KI [auth 51],
KJ [auth 81],
LC [auth 51],
LD [auth 51],
LE [auth 51],
LF [auth 51],
LG [auth 51],
LH [auth 51],
LI [auth 51],
LJ [auth 81],
MC [auth 51],
MD [auth 51],
ME [auth 51],
MF [auth 51],
MG [auth 51],
MH [auth 51],
MI [auth 51],
MJ [auth 81],
NC [auth 51],
ND [auth 51],
NE [auth 51],
NF [auth 51],
NG [auth 51],
NH [auth 51],
NI [auth 51],
NJ [auth A1],
OC [auth 51],
OD [auth 51],
OE [auth 51],
OF [auth 51],
OG [auth 51],
OH [auth 51],
OI [auth 51],
OJ [auth A1],
PC [auth 51],
PD [auth 51],
PE [auth 51],
PF [auth 51],
PG [auth 51],
PH [auth 51],
PI [auth 51],
PJ [auth B1],
QC [auth 51],
QD [auth 51],
QE [auth 51],
QF [auth 51],
QG [auth 51],
QH [auth 51],
QI [auth 51],
QJ [auth V1],
RC [auth 51],
RD [auth 51],
RE [auth 51],
RF [auth 51],
RG [auth 51],
RH [auth 51],
RI [auth 51],
SC [auth 51],
SD [auth 51],
SE [auth 51],
SF [auth 51],
SG [auth 51],
SH [auth 51],
SI [auth 51],
SJ [auth b1],
TC [auth 51],
TD [auth 51],
TE [auth 51],
TF [auth 51],
TG [auth 51],
TH [auth 51],
TI [auth 51],
UC [auth 51],
UD [auth 51],
UE [auth 51],
UF [auth 51],
UG [auth 51],
UH [auth 51],
UI [auth 51],
UJ [auth e1],
VC [auth 51],
VD [auth 51],
VE [auth 51],
VF [auth 51],
VG [auth 51],
VH [auth 51],
VI [auth 51],
WC [auth 51],
WD [auth 51],
WE [auth 51],
WF [auth 51],
WG [auth 51],
WH [auth 51],
WI [auth 51],
XC [auth 51],
XD [auth 51],
XE [auth 51],
XF [auth 51],
XG [auth 51],
XH [auth 51],
XI [auth 51],
XJ [auth m1],
YC [auth 51],
YD [auth 51],
YE [auth 51],
YF [auth 51],
YG [auth 51],
YH [auth 51],
YI [auth 51],
ZB [auth 51],
ZC [auth 51],
ZD [auth 51],
ZE [auth 51],
ZF [auth 51],
ZG [auth 51],
ZH [auth 51],
ZI [auth 51]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.14
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Research Promotion AgencyAustriaFFG-852936
Austrian Science FundAustriaSTART Projekt Y 1031-B28
Austrian Science FundAustriaSFB RNA-Deco F 80
Swiss National Science FoundationSwitzerlandP2GEP3_191204
European Molecular Biology Organization (EMBO)ALTF 1165-2019

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references
  • Version 1.2: 2023-02-01
    Changes: Database references
  • Version 1.3: 2023-02-08
    Changes: Database references
  • Version 1.4: 2024-07-17
    Changes: Data collection