7OYB image
Entry Detail
PDB ID:
7OYB
EMDB ID:
Keywords:
Title:
Cryo-EM structure of the 6 hpf zebrafish embryo 80S ribosome
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2021-06-24
Release Date:
2022-07-13
Method Details:
Experimental Method:
Resolution:
2.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:18S rRNA
Chain IDs:A (auth: 22)
Chain Length:1939
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polyribonucleotide
Description:28S rRNA
Chain IDs:B (auth: 51)
Chain Length:4269
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:C (auth: 71)
Chain Length:120
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polyribonucleotide
Description:5.8S rRNA
Chain IDs:D (auth: 81)
Chain Length:158
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8
Chain IDs:E (auth: A1)
Chain Length:257
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein SA
Chain IDs:F (auth: A2)
Chain Length:115
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein L3
Chain IDs:G (auth: B1)
Chain Length:403
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3a
Chain IDs:H (auth: B2)
Chain Length:84
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein L4
Chain IDs:I (auth: C1)
Chain Length:375
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S2
Chain IDs:J (auth: C2)
Chain Length:69
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein L5b
Chain IDs:K (auth: D1)
Chain Length:123
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:DNA-(apurinic or apyrimidinic site) lyase
Chain IDs:L (auth: D2)
Chain Length:245
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6
Chain IDs:M (auth: E1)
Chain Length:135
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S4, X isoform
Chain IDs:N (auth: E2)
Chain Length:133
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein L7
Chain IDs:O (auth: F1)
Chain Length:110
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein S5
Chain IDs:P (auth: F2)
Chain Length:204
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7a
Chain IDs:Q (auth: G1)
Chain Length:117
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S6
Chain IDs:R (auth: G2)
Chain Length:249
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9
Chain IDs:S (auth: H1)
Chain Length:123
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S7
Chain IDs:T (auth: H2)
Chain Length:194
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L10
Chain IDs:U (auth: I1)
Chain Length:215
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S8
Chain IDs:V (auth: I2)
Chain Length:208
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L11
Chain IDs:W (auth: J1)
Chain Length:97
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S9
Chain IDs:X (auth: J2)
Chain Length:194
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein S10
Chain IDs:Y (auth: K2)
Chain Length:166
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13
Chain IDs:Z (auth: L1)
Chain Length:50
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S11
Chain IDs:AA (auth: L2)
Chain Length:159
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14
Chain IDs:BA (auth: M1)
Chain Length:128
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein L15
Chain IDs:CA (auth: N1)
Chain Length:25
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S13
Chain IDs:DA (auth: N2)
Chain Length:151
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13a
Chain IDs:EA (auth: O1)
Chain Length:205
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein S14
Chain IDs:FA (auth: O2)
Chain Length:151
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17
Chain IDs:GA (auth: P1)
Chain Length:92
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15
Chain IDs:HA (auth: P2)
Chain Length:145
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein L18
Chain IDs:IA (auth: Q1)
Chain Length:182
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein S16
Chain IDs:JA (auth: Q2)
Chain Length:146
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19
Chain IDs:KA (auth: R1)
Chain Length:138
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S17
Chain IDs:LA (auth: R2)
Chain Length:134
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18a
Chain IDs:MA (auth: S1)
Chain Length:176
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S18
Chain IDs:NA (auth: S2)
Chain Length:152
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21
Chain IDs:OA (auth: T1)
Chain Length:160
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S19
Chain IDs:PA (auth: T2)
Chain Length:146
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein L22
Chain IDs:QA (auth: U1)
Chain Length:141
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S20
Chain IDs:RA (auth: U2)
Chain Length:119
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23
Chain IDs:SA (auth: V1)
Chain Length:140
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S21
Chain IDs:TA (auth: V2)
Chain Length:81
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L24
Chain IDs:UA (auth: W1)
Chain Length:157
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15a
Chain IDs:VA (auth: W2)
Chain Length:130
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein L23a
Chain IDs:WA (auth: X1)
Chain Length:155
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S23
Chain IDs:XA (auth: X2)
Chain Length:143
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:ATPase H+ transporting V0 subunit e1
Chain IDs:YA (auth: Y1)
Chain Length:145
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S24
Chain IDs:ZA (auth: Y2)
Chain Length:132
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27
Chain IDs:AB (auth: Z1)
Chain Length:136
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S25
Chain IDs:BB (auth: Z2)
Chain Length:124
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27a
Chain IDs:CB (auth: a1)
Chain Length:257
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S26
Chain IDs:DB (auth: a2)
Chain Length:115
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:EB (auth: b1)
Chain Length:403
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27
Chain IDs:FB (auth: b2)
Chain Length:84
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L30
Chain IDs:GB (auth: c1)
Chain Length:375
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S28
Chain IDs:HB (auth: c2)
Chain Length:69
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31
Chain IDs:IB (auth: d1)
Chain Length:123
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S29
Chain IDs:JB (auth: d2)
Chain Length:245
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein L32
Chain IDs:KB (auth: e1)
Chain Length:135
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S30
Chain IDs:LB (auth: e2)
Chain Length:133
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35a
Chain IDs:MB (auth: f1)
Chain Length:110
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34
Chain IDs:NB (auth: g1)
Chain Length:117
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Guanine nucleotide-binding protein subunit beta-2-like 1
Chain IDs:OB (auth: g2)
Chain Length:249
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35
Chain IDs:PB (auth: h1)
Chain Length:123
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36
Chain IDs:QB (auth: i1)
Chain Length:215
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein L37
Chain IDs:RB (auth: j1)
Chain Length:97
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:SB (auth: k1)
Chain Length:70
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Ribosomal protein L39
Chain IDs:TB (auth: l1)
Chain Length:50
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L40
Chain IDs:UB (auth: m1)
Chain Length:128
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Rpl41
Chain IDs:VB (auth: n1)
Chain Length:25
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36a
Chain IDs:WB (auth: o1)
Chain Length:205
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:Zgc:171772
Chain IDs:XB (auth: p1)
Chain Length:92
Number of Molecules:1
Biological Source:Danio rerio
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28
Chain IDs:YB (auth: r1)
Chain Length:138
Number of Molecules:1
Biological Source:Danio rerio
Primary Citation
A molecular network of conserved factors keeps ribosomes dormant in the egg.
Nature 613 712 720 (2023)
PMID: 36653451 DOI: 10.1038/s41586-022-05623-y

Abstact

Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed1-4. 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.

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Primary Citation of related structures