7ZJW image
Entry Detail
PDB ID:
7ZJW
EMDB ID:
Keywords:
Title:
Rabbit 80S ribosome as it decodes the Sec-UGA codon
Biological Source:
PDB Version:
Deposition Date:
2022-04-12
Release Date:
2022-10-19
Method Details:
Experimental Method:
Resolution:
2.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:SECIS Binding Protein 2
Chain IDs:E (auth: B)
Chain Length:854
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:eEFSec
Chain IDs:A (auth: E)
Chain Length:616
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:human Ser-tRNA-Sec
Chain IDs:B (auth: F)
Chain Length:90
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:CrPV IRES
Chain IDs:C (auth: I)
Chain Length:1072
Number of Molecules:1
Biological Source:Cricket paralysis virus
Polymer Type:polyribonucleotide
Description:28S rRNA
Chain IDs:F (auth: L5)
Chain Length:4808
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:G (auth: L7)
Chain Length:119
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Description:5.8S rRNA
Chain IDs:H (auth: L8)
Chain Length:158
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein uL2
Chain IDs:I (auth: LD)
Chain Length:148
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:J (auth: LE)
Chain Length:245
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4
Chain IDs:K (auth: LF)
Chain Length:413
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal_L18_c domain-containing protein
Chain IDs:L (auth: LG)
Chain Length:297
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6
Chain IDs:M (auth: LH)
Chain Length:135
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal Protein uL30
Chain IDs:N (auth: LI)
Chain Length:110
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL8
Chain IDs:O (auth: LJ)
Chain Length:266
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9
Chain IDs:P (auth: LK)
Chain Length:123
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L10
Chain IDs:Q (auth: LL)
Chain Length:214
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L11
Chain IDs:R (auth: LM)
Chain Length:178
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL13
Chain IDs:S (auth: LO)
Chain Length:51
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14
Chain IDs:T (auth: LP)
Chain Length:218
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L15
Chain IDs:U (auth: LQ)
Chain Length:204
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein uL13
Chain IDs:V (auth: LR)
Chain Length:203
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein uL22
Chain IDs:W (auth: LS)
Chain Length:184
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal Protein eL18
Chain IDs:X (auth: LT)
Chain Length:188
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19
Chain IDs:Y (auth: LU)
Chain Length:196
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL20
Chain IDs:Z (auth: LV)
Chain Length:176
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL21
Chain IDs:AA (auth: LW)
Chain Length:160
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL22
Chain IDs:BA (auth: LX)
Chain Length:217
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23
Chain IDs:CA (auth: LY)
Chain Length:140
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL24
Chain IDs:DA (auth: LZ)
Chain Length:157
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein uL23
Chain IDs:EA (auth: La)
Chain Length:156
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26
Chain IDs:FA (auth: Lb)
Chain Length:145
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27
Chain IDs:GA (auth: Lc)
Chain Length:136
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27a
Chain IDs:HA (auth: Ld)
Chain Length:148
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:IA (auth: Le)
Chain Length:245
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL30
Chain IDs:JA (auth: Lf)
Chain Length:413
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL31
Chain IDs:KA (auth: Lg)
Chain Length:297
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL32
Chain IDs:LA (auth: Lh)
Chain Length:135
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL33
Chain IDs:MA (auth: Li)
Chain Length:110
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34
Chain IDs:NA (auth: Lj)
Chain Length:266
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein uL29
Chain IDs:OA (auth: Lk)
Chain Length:123
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36
Chain IDs:PA (auth: Ll)
Chain Length:214
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37
Chain IDs:QA (auth: Lm)
Chain Length:178
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL38
Chain IDs:RA (auth: Ln)
Chain Length:70
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL39
Chain IDs:SA (auth: Lo)
Chain Length:51
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L40
Chain IDs:TA (auth: Lp)
Chain Length:218
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL42
Chain IDs:UA (auth: Lq)
Chain Length:204
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL43
Chain IDs:VA (auth: Lr)
Chain Length:203
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL28
Chain IDs:WA (auth: Ls)
Chain Length:184
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein P0
Chain IDs:XA (auth: Lt)
Chain Length:188
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein uL1
Chain IDs:YA (auth: Lx)
Chain Length:217
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Description:GPX4 SECIS element
Chain IDs:D (auth: S)
Chain Length:855
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polyribonucleotide
Description:18S rRNA
Chain IDs:ZA (auth: S2)
Chain Length:1870
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27
Chain IDs:AB (auth: SB)
Chain Length:172
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S28
Chain IDs:BB (auth: SC)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27a
Chain IDs:CB (auth: SD)
Chain Length:152
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S30
Chain IDs:DB (auth: SE)
Chain Length:133
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal protein eS26
Chain IDs:EB (auth: SF)
Chain Length:115
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:RACK1
Chain IDs:FB (auth: SG)
Chain Length:317
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein uS14
Chain IDs:GB (auth: SH)
Chain Length:56
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein SA
Chain IDs:HB (auth: SL)
Chain Length:295
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3a
Chain IDs:IB (auth: SM)
Chain Length:264
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein uS5
Chain IDs:JB (auth: SN)
Chain Length:293
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3
Chain IDs:KB (auth: SO)
Chain Length:281
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein eS4
Chain IDs:LB (auth: SP)
Chain Length:263
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Ribosomal protein S5
Chain IDs:MB (auth: SQ)
Chain Length:204
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S6
Chain IDs:NB (auth: SR)
Chain Length:249
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S7
Chain IDs:OB (auth: SS)
Chain Length:432
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S8
Chain IDs:PB (auth: ST)
Chain Length:208
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S9
Chain IDs:QB (auth: SU)
Chain Length:194
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein eS10
Chain IDs:RB (auth: SV)
Chain Length:165
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S11
Chain IDs:SB (auth: SW)
Chain Length:158
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S12
Chain IDs:TB (auth: SX)
Chain Length:132
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein uS15
Chain IDs:UB (auth: SY)
Chain Length:151
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein uS11
Chain IDs:VB (auth: SZ)
Chain Length:151
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein uS19
Chain IDs:WB (auth: Sa)
Chain Length:145
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein uS9
Chain IDs:XB (auth: Sb)
Chain Length:172
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein eS17
Chain IDs:YB (auth: Sc)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S18
Chain IDs:ZB (auth: Sd)
Chain Length:152
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S Ribosomal protein eS19
Chain IDs:AC (auth: Se)
Chain Length:133
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein uS10
Chain IDs:BC (auth: Sf)
Chain Length:115
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein eS21
Chain IDs:CC (auth: Sg)
Chain Length:317
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15a
Chain IDs:DC (auth: Sh)
Chain Length:56
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S23
Chain IDs:EC (auth: Si)
Chain Length:143
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S24
Chain IDs:FC (auth: Sj)
Chain Length:130
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S25
Chain IDs:GC (auth: Sk)
Chain Length:124
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L41
Chain IDs:HC (auth: Sl)
Chain Length:295
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
6MZ ZA A modified residue
7MG ZA G modified residue
A2M ZA A modified residue
AME CC MET modified residue
AYA K ALA modified residue
HIC J HIS modified residue
HY3 EC PRO modified residue
M3L TA LYS modified residue
MA6 ZA A modified residue
MLZ IA LYS modified residue
NMM AC ARG modified residue
OMC ZA C modified residue
OMG H G modified residue
OMU ZA U modified residue
PSU H U modified residue
SAC WA SER modified residue
Primary Citation
Structure of the mammalian ribosome as it decodes the selenocysteine UGA codon.
Science 376 1338 1343 (2022)
PMID: 35709277 DOI: 10.1126/science.abg3875

Abstact

The elongation of eukaryotic selenoproteins relies on a poorly understood process of interpreting in-frame UGA stop codons as selenocysteine (Sec). We used cryo-electron microscopy to visualize Sec UGA recoding in mammals. A complex between the noncoding Sec-insertion sequence (SECIS), SECIS-binding protein 2 (SBP2), and 40S ribosomal subunit enables Sec-specific elongation factor eEFSec to deliver Sec. eEFSec and SBP2 do not interact directly but rather deploy their carboxyl-terminal domains to engage with the opposite ends of the SECIS. By using its Lys-rich and carboxyl-terminal segments, the ribosomal protein eS31 simultaneously interacts with Sec-specific transfer RNA (tRNASec) and SBP2, which further stabilizes the assembly. eEFSec is indiscriminate toward l-serine and facilitates its misincorporation at Sec UGA codons. Our results support a fundamentally distinct mechanism of Sec UGA recoding in eukaryotes from that in bacteria.

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Primary Citation of related structures