8JIW image
Entry Detail
PDB ID:
8JIW
EMDB ID:
Keywords:
Title:
Atomic structure of wheat ribosome reveals unique features of the plant ribosomes
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2023-05-28
Release Date:
2024-03-27
Method Details:
Experimental Method:
Resolution:
2.88 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:18S rRNA
Chain IDs:A (auth: Ad)
Chain Length:1811
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein SA
Chain IDs:B (auth: BA)
Chain Length:139
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3a
Chain IDs:C (auth: BB)
Chain Length:263
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:S5 DRBM domain-containing protein
Chain IDs:D (auth: BC)
Chain Length:65
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:KH type-2 domain-containing protein
Chain IDs:V (auth: BD)
Chain Length:227
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S4
Chain IDs:E (auth: BE)
Chain Length:62
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:Ribosomal protein S7 domain-containing protein
Chain IDs:W (auth: BF)
Chain Length:200
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S6
Chain IDs:F (auth: BG)
Chain Length:250
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S7
Chain IDs:G (auth: BH)
Chain Length:192
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S8
Chain IDs:H (auth: BI)
Chain Length:224
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4, chloroplastic
Chain IDs:I (auth: BJ)
Chain Length:195
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:Plectin/S10 N-terminal domain-containing protein
Chain IDs:X (auth: BK)
Chain Length:188
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S11 N-terminal domain-containing protein
Chain IDs:J (auth: BL)
Chain Length:161
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:Ribosomal protein S13/S15 N-terminal domain-containing protein
Chain IDs:K (auth: BN)
Chain Length:151
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S14
Chain IDs:L (auth: BO)
Chain Length:151
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15
Chain IDs:Y (auth: BP)
Chain Length:153
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S16
Chain IDs:Z (auth: BQ)
Chain Length:149
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S17
Chain IDs:M (auth: BR)
Chain Length:143
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S18
Chain IDs:AA (auth: BS)
Chain Length:152
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S19
Chain IDs:BA (auth: BT)
Chain Length:155
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:Ribosomal protein S10 domain-containing protein
Chain IDs:CA (auth: BU)
Chain Length:117
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S21
Chain IDs:N (auth: BV)
Chain Length:82
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8, chloroplastic
Chain IDs:O (auth: BW)
Chain Length:130
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S23
Chain IDs:P (auth: BX)
Chain Length:142
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S24
Chain IDs:Q (auth: BY)
Chain Length:137
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S25
Chain IDs:GA (auth: BZ)
Chain Length:98
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S26
Chain IDs:R (auth: Ba)
Chain Length:139
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27
Chain IDs:S (auth: Bb)
Chain Length:263
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S28
Chain IDs:DA (auth: Bc)
Chain Length:65
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S29
Chain IDs:EA (auth: Bd)
Chain Length:227
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S30
Chain IDs:T (auth: Be)
Chain Length:62
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:Mitogen-activated protein kinase
Chain IDs:FA (auth: Bg)
Chain Length:250
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L41
Chain IDs:U (auth: Cn)
Chain Length:25
Number of Molecules:1
Biological Source:Triticum aestivum
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
A2M A A modified residue
MA6 A A modified residue
OMC A C modified residue
OMG A G modified residue
OMU A U modified residue
PSU A U modified residue
Primary Citation
Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes.
Structure 32 562 ? (2024)
PMID: 38458197 DOI: 10.1016/j.str.2024.02.006

Abstact

Plants being sessile organisms exhibit unique features in ribosomes, which might aid in rapid gene expression and regulation in response to varying environmental conditions. Here, we present high-resolution structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in the peptide exit tunnel (PET), the zinc-finger motif in eL34 is absent, and uL4 is extended, making an exclusive interaction network. We note differences in the eL15-helix 11 (25S) interaction, eL6-ES7 assembly, and certain rRNA chemical modifications between monocot and dicot ribosomes. In eukaryotes, we observe highly conserved rRNA modification (Gm75) in 5.8S rRNA and a flipped base (G1506) in PET. These features are likely involved in sensing or stabilizing nascent chain. Finally, we discuss the importance of the universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.

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Primary Citation of related structures