8Q7Z image
Entry Detail
PDB ID:
8Q7Z
EMDB ID:
Keywords:
Title:
Structure of the G. gallus 80S non-rotated ribosome
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2023-08-17
Release Date:
2024-08-28
Method Details:
Experimental Method:
Resolution:
2.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:18S rRNA
Chain IDs:TA (auth: A2)
Chain Length:1823
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27
Chain IDs:VA (auth: AA)
Chain Length:84
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S28
Chain IDs:WA (auth: AB)
Chain Length:69
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ubiquitin
Chain IDs:PB (auth: AC)
Chain Length:156
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein eS30
Chain IDs:ZA (auth: AD)
Chain Length:133
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S26
Chain IDs:AB (auth: AE)
Chain Length:204
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein RACK1
Chain IDs:RB (auth: AF)
Chain Length:317
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S29
Chain IDs:SB (auth: AG)
Chain Length:171
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS2
Chain IDs:NB (auth: AZ)
Chain Length:25
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS1
Chain IDs:UA (auth: Aa)
Chain Length:84
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S2
Chain IDs:XA (auth: Ab)
Chain Length:69
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:DNA-(apurinic or apyrimidinic site) lyase
Chain IDs:ZB (auth: Ac)
Chain Length:156
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS4
Chain IDs:YA (auth: Ad)
Chain Length:133
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein S5
Chain IDs:QB (auth: Ae)
Chain Length:204
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS6
Chain IDs:BB (auth: Af)
Chain Length:317
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S7
Chain IDs:CB (auth: Ag)
Chain Length:171
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S8
Chain IDs:DB (auth: Ah)
Chain Length:207
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S9
Chain IDs:EB (auth: Ai)
Chain Length:194
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein S10
Chain IDs:TB (auth: Aj)
Chain Length:165
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S11
Chain IDs:FB (auth: Ak)
Chain Length:158
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS12
Chain IDs:UB (auth: Al)
Chain Length:132
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS15
Chain IDs:GB (auth: Am)
Chain Length:151
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein S14
Chain IDs:HB (auth: An)
Chain Length:151
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS19
Chain IDs:VB (auth: Ao)
Chain Length:145
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein S16
Chain IDs:OB (auth: Ap)
Chain Length:146
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS17
Chain IDs:BC (auth: Aq)
Chain Length:135
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S18
Chain IDs:WB (auth: Ar)
Chain Length:152
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S19
Chain IDs:XB (auth: As)
Chain Length:145
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S20
Chain IDs:IB (auth: At)
Chain Length:119
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS21
Chain IDs:JB (auth: Au)
Chain Length:83
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15a
Chain IDs:KB (auth: Av)
Chain Length:130
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS12
Chain IDs:LB (auth: Aw)
Chain Length:143
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S24
Chain IDs:MB (auth: Ax)
Chain Length:131
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S25
Chain IDs:YB (auth: Ay)
Chain Length:125
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L41
Chain IDs:D (auth: Az)
Chain Length:25
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polyribonucleotide
Description:28S rRNA
Chain IDs:A (auth: B5)
Chain Length:4441
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:C (auth: B7)
Chain Length:119
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polyribonucleotide
Description:5.8S rRNA
Chain IDs:B (auth: B8)
Chain Length:157
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8
Chain IDs:E (auth: BA)
Chain Length:257
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL3
Chain IDs:F (auth: BB)
Chain Length:71
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4 C-terminal domain-containing protein
Chain IDs:G (auth: BC)
Chain Length:421
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL18
Chain IDs:H (auth: BD)
Chain Length:176
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6
Chain IDs:I (auth: BE)
Chain Length:135
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL30
Chain IDs:J (auth: BF)
Chain Length:110
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein eL8
Chain IDs:K (auth: BG)
Chain Length:266
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9
Chain IDs:L (auth: BH)
Chain Length:123
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL16
Chain IDs:M (auth: BI)
Chain Length:214
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L11
Chain IDs:N (auth: BJ)
Chain Length:178
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein eL13
Chain IDs:O (auth: BL)
Chain Length:211
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14
Chain IDs:P (auth: BM)
Chain Length:131
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L15
Chain IDs:Q (auth: BN)
Chain Length:204
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL13
Chain IDs:R (auth: BO)
Chain Length:203
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17
Chain IDs:S (auth: BP)
Chain Length:92
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L18
Chain IDs:T (auth: BQ)
Chain Length:187
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L19
Chain IDs:U (auth: BR)
Chain Length:196
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18a
Chain IDs:V (auth: BS)
Chain Length:176
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21
Chain IDs:W (auth: BT)
Chain Length:160
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein eL22
Chain IDs:X (auth: BU)
Chain Length:128
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL14
Chain IDs:Y (auth: BV)
Chain Length:140
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L24
Chain IDs:Z (auth: BW)
Chain Length:157
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL23
Chain IDs:AA (auth: BX)
Chain Length:155
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L26 like 1
Chain IDs:BA (auth: BY)
Chain Length:145
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein eL27
Chain IDs:CA (auth: BZ)
Chain Length:136
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL15
Chain IDs:DA (auth: Ba)
Chain Length:257
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:EA (auth: Bb)
Chain Length:71
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein eL30
Chain IDs:FA (auth: Bc)
Chain Length:421
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31
Chain IDs:GA (auth: Bd)
Chain Length:176
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L32
Chain IDs:HA (auth: Be)
Chain Length:135
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35a
Chain IDs:IA (auth: Bf)
Chain Length:110
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34
Chain IDs:JA (auth: Bg)
Chain Length:266
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL29
Chain IDs:KA (auth: Bh)
Chain Length:123
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein eL36
Chain IDs:LA (auth: Bi)
Chain Length:214
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L37
Chain IDs:MA (auth: Bj)
Chain Length:178
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:NA (auth: Bk)
Chain Length:70
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein eL39
Chain IDs:OA (auth: Bl)
Chain Length:211
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ubiquitin-60S ribosomal protein L40
Chain IDs:PA (auth: Bm)
Chain Length:131
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Ribosomal protein L36a like
Chain IDs:QA (auth: Bo)
Chain Length:203
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein eL43
Chain IDs:RA (auth: Bp)
Chain Length:92
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28
Chain IDs:SA (auth: Br)
Chain Length:196
Number of Molecules:1
Biological Source:Gallus gallus
Polymer Type:polyribonucleotide
Description:Phe tRNA
Chain IDs:AC (auth: V)
Chain Length:76
Number of Molecules:1
Biological Source:Gallus gallus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MA A A modified residue
5MC A C modified residue
6MZ A A modified residue
A2M A A modified residue
AME JB MET modified residue
HIC F HIS modified residue
MA6 TA A modified residue
MLZ QA LYS modified residue
OMC A C modified residue
OMG A G modified residue
OMU A U modified residue
PSU A U modified residue
SAC NB SER modified residue
UR3 A U modified residue
Primary Citation
Cryo-EM structure of the inactive ribosome complex accumulated in chick embryo cells in cold-stress conditions.
Febs Lett. 598 537 547 (2024)
PMID: 38395592 DOI: 10.1002/1873-3468.14831

Abstact

Here, we present the high-resolution structure of the Gallus gallus 80S ribosome obtained from cold-treated chicken embryos. The translationally inactive ribosome complex contains elongation factor eEF2 with GDP, SERPINE1 mRNA binding protein 1 (SERBP1) and deacylated tRNA in the P/E position, showing common features with complexes already described in mammals. Modeling of most expansion segments of G. gallus 28S ribosomal RNA allowed us to identify specific features in their structural organization and to describe areas where a marked difference between mammalian and avian ribosomes could shed light on the evolution of the expansion segments. This study provides the first structure of an avian ribosome, establishing a model for future structural and functional studies on the translational machinery in Aves.

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Primary Citation of related structures