7OYC

Cryo-EM structure of the Xenopus egg 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 1.2 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: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5AA [auth 11]154Xenopus laevisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8F [auth A1]257Xenopus laevisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAG [auth A2]306Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q7ZX07 (Xenopus laevis)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Rpl3-prov proteinH [auth B1]403Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3a-AI [auth B2]264Xenopus laevisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-BJ [auth C1]401Xenopus laevisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2K [auth C2]281Xenopus laevisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Rpl5-b proteinL [auth D1]296Xenopus laevisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-(apurinic or apyrimidinic site) lyaseM [auth D2]246Xenopus laevisMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6N [auth E1]258Xenopus laevisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4O [auth E2]263Xenopus laevisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
MGC130910 proteinP [auth F1]246Xenopus laevisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_S7 domain-containing proteinQ [auth F2]203Xenopus laevisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aR [auth G1]266Xenopus laevisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6S [auth G2]249Xenopus laevisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9T [auth H1]192Xenopus laevisMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7U [auth H2]194Xenopus laevisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L16 domain-containing proteinV [auth I1]215Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8W [auth I2]208Xenopus laevisMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11X [auth J1]177Xenopus laevisMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9Y [auth J2]194Xenopus laevisMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10Z [auth K2]165Xenopus laevisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13AA [auth L1]211Xenopus laevisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11BA [auth L2]158Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14CA [auth M1]138Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15DA [auth N1]204Xenopus laevisMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13EA [auth N2]151Xenopus laevisMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aFA [auth O1]231Xenopus laevisMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Rps14GA [auth O2]151Xenopus laevisMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17HA [auth P1]184Xenopus laevisMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15IA [auth P2]145Xenopus laevisMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L18e/L15P domain-containing proteinJA [auth Q1]188Xenopus laevisMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Rps16 proteinKA [auth Q2]146Xenopus laevisMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19LA [auth R1]197Xenopus laevisMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17MA [auth R2]135Xenopus laevisMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aNA [auth S1]176Xenopus laevisMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18OA [auth S2]152Xenopus laevisMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21PA [auth T1]160Xenopus laevisMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19QA [auth T2]146Xenopus laevisMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22RA [auth U1]128Xenopus laevisMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20SA [auth U2]119Xenopus laevisMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23TA [auth V1]140Xenopus laevisMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21UA [auth V2]83Xenopus laevisMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
TRASH domain-containing proteinVA [auth W1]155Xenopus laevisMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aWA [auth W2]130Xenopus laevisMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L23eN domain-containing proteinXA [auth X1]155Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23YA [auth X2]143Xenopus laevisMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
KOW domain-containing proteinZA [auth Y1]145Xenopus laevisMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24AB [auth Y2]132Xenopus laevisMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27BB [auth Z1]136Xenopus laevisMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25CB [auth Z2]125Xenopus laevisMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aDB [auth a1]148Xenopus laevisMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26EB [auth a2]115Xenopus laevisMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29FB [auth b1]75Xenopus laevisMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27GB [auth b2]84Xenopus laevisMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30HB [auth c1]116Xenopus laevisMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28IB [auth c2]69Xenopus laevisMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31JB [auth d1]125Xenopus laevisMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29KB [auth d2]86Xenopus laevisMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Rpl32LB [auth e1]135Xenopus laevisMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30MB [auth e2]133Xenopus laevisMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aNB [auth f1]110Xenopus laevisMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34OB [auth g1]117Xenopus laevisMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Gnb2l1-prov proteinPB [auth g2]317Xenopus laevisMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35QB [auth h1]123Xenopus laevisMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36RB [auth i1]105Xenopus laevisMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
HABP4_PAI-RBP1 domain-containing proteinSB [auth i2]378Xenopus laevisMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37TB [auth j1]97Xenopus laevisMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38UB [auth k1]70Xenopus laevisMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
MGC116452 proteinVB [auth l1]51Xenopus laevisMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40WB [auth m1]128Xenopus laevisMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Rpl41XB [auth n1]25Xenopus laevisMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
MGC85428 proteinYB [auth o1]106Xenopus laevisMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Rpl37aZB [auth p1]92Xenopus laevisMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28AC [auth r1]137Xenopus laevisMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Death-associated protein-like 1-BBC [auth s1]113Xenopus laevisMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Eef2-prov proteinCC [auth v2]858Xenopus laevisMutation(s): 0 
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S rRNAB [auth 22]1,826Xenopus laevis
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Entity ID: 3
MoleculeChains LengthOrganismImage
28S rRNAC [auth 51]4,115Xenopus laevis
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Entity ID: 4
MoleculeChains LengthOrganismImage
5S rRNAD [auth 71]120Xenopus laevis
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Entity ID: 5
MoleculeChains LengthOrganismImage
5.8S rRNAE [auth 81]156Xenopus laevis
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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FH [auth a2]
GH [auth d2]
IH [auth g1]
JH [auth j1]
LH [auth m1]
FH [auth a2],
GH [auth d2],
IH [auth g1],
JH [auth j1],
LH [auth m1],
MH [auth o1],
NH [auth p1]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AD [auth 51]
AE [auth 51]
AF [auth 51]
AG [auth 51]
AH [auth A1]
AD [auth 51],
AE [auth 51],
AF [auth 51],
AG [auth 51],
AH [auth A1],
BD [auth 51],
BE [auth 51],
BF [auth 51],
BG [auth 51],
BH [auth B1],
CD [auth 51],
CE [auth 51],
CF [auth 51],
CG [auth 51],
CH [auth C1],
DC [auth 51],
DD [auth 51],
DE [auth 51],
DF [auth 51],
DG [auth 51],
DH [auth V1],
EC [auth 51],
ED [auth 51],
EE [auth 51],
EF [auth 51],
EG [auth 51],
EH [auth a1],
FC [auth 51],
FD [auth 51],
FE [auth 51],
FF [auth 51],
FG [auth 51],
GC [auth 51],
GD [auth 51],
GE [auth 51],
GF [auth 51],
GG [auth 51],
HC [auth 51],
HD [auth 51],
HE [auth 51],
HF [auth 51],
HG [auth 51],
HH [auth e1],
IC [auth 51],
ID [auth 51],
IE [auth 51],
IF [auth 51],
IG [auth 51],
JC [auth 51],
JD [auth 51],
JE [auth 51],
JF [auth 51],
JG [auth 51],
KC [auth 51],
KD [auth 51],
KE [auth 51],
KF [auth 51],
KG [auth 51],
KH [auth m1],
LC [auth 51],
LD [auth 51],
LE [auth 51],
LF [auth 51],
LG [auth 51],
MC [auth 51],
MD [auth 51],
ME [auth 51],
MF [auth 51],
MG [auth 51],
NC [auth 51],
ND [auth 51],
NE [auth 51],
NF [auth 51],
NG [auth 51],
OC [auth 51],
OD [auth 51],
OE [auth 51],
OF [auth 51],
OG [auth 51],
PC [auth 51],
PD [auth 51],
PE [auth 51],
PF [auth 51],
PG [auth 51],
QC [auth 51],
QD [auth 51],
QE [auth 51],
QF [auth 51],
QG [auth 51],
RC [auth 51],
RD [auth 51],
RE [auth 51],
RF [auth 51],
RG [auth 51],
SC [auth 51],
SD [auth 51],
SE [auth 51],
SF [auth 51],
SG [auth 51],
TC [auth 51],
TD [auth 51],
TE [auth 51],
TF [auth 51],
TG [auth 51],
UC [auth 51],
UD [auth 51],
UE [auth 51],
UF [auth 51],
UG [auth 51],
VC [auth 51],
VD [auth 51],
VE [auth 51],
VF [auth 51],
VG [auth 51],
WC [auth 51],
WD [auth 51],
WE [auth 51],
WF [auth 51],
WG [auth 71],
XC [auth 51],
XD [auth 51],
XE [auth 51],
XF [auth 51],
XG [auth 71],
YC [auth 51],
YD [auth 51],
YE [auth 51],
YF [auth 51],
YG [auth 81],
ZC [auth 51],
ZD [auth 51],
ZE [auth 51],
ZF [auth 51],
ZG [auth 81]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
5CT
Query on 5CT
A [auth 11]PEPTIDE LINKINGC10 H23 N3 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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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: 2022-07-20
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2023-02-08
    Changes: Database references