8JIW image
Deposition Date 2023-05-28
Release Date 2024-03-27
Last Version Date 2025-02-12
Entry Detail
PDB ID:
8JIW
Keywords:
TRANSLATION
Title:
Atomic structure of wheat ribosome reveals unique features of the plant ribosomes
Biological Source:
Source Organism:
Triticum aestivum (Taxon ID: 4565)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.88 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8JIW validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:A (auth: Ad)
Chain Length:1811
Number of Molecules:1
Biological Source:Triticum aestivum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):CFC21_016030
Chain IDs:B (auth: BA)
Chain Length:139
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6AV88 Pfam ID:PF00318, PF16122
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):CFC21_058573
Chain IDs:C (auth: BB)
Chain Length:263
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6IU74 Pfam ID:PF01015
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:S5 DRBM domain-containing protein
Gene (Uniprot):CFC21_080285
Chain IDs:D (auth: BC)
Chain Length:65
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6N0N5 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:KH type-2 domain-containing protein
Gene (Uniprot):CFC21_034353, CFC21_034354, CFC21_109361
Chain IDs:V (auth: BD)
Chain Length:227
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5I1R7 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Gene (Uniprot):CFC21_005863, CFC21_010690
Chain IDs:E (auth: BE)
Chain Length:62
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A1D5SLI4 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S7 domain-containing protein
Chain IDs:W (auth: BF)
Chain Length:200
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A9R1JSD6
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):CAMPLR22A2D_LOCUS542, CFC21_015030, CFC21_021276, CFC21_021277
Chain IDs:F (auth: BG)
Chain Length:250
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5C8N6 Pfam ID:PF01092
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):LOC123092417
Chain IDs:G (auth: BH)
Chain Length:192
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:Q5I7K2 Pfam ID:PF01251
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):CFC21_023528
Chain IDs:H (auth: BI)
Chain Length:224
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6C6G0 Pfam ID:PF01201
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4, chloroplastic
Gene (Uniprot):CFC21_011030, CFC21_064815, CFC21_070616
Chain IDs:I (auth: BJ)
Chain Length:195
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5FPA7 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Plectin/S10 N-terminal domain-containing protein
Gene (Uniprot):CFC21_017397
Chain IDs:X (auth: BK)
Chain Length:188
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5AUH7 Pfam ID:PF03501
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11 N-terminal domain-containing protein
Gene (Uniprot):CFC21_092816
Chain IDs:J (auth: BL)
Chain Length:161
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6QHW3 Pfam ID:PF16205, PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S13/S15 N-terminal domain-containing protein
Gene (Uniprot):CFC21_054424, CFC21_098222, CFC21_103236, CFC21_103237, CFC21_103240, CFC21_109586
Chain IDs:K (auth: BN)
Chain Length:151
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5I035 Pfam ID:PF08069, PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Gene (Uniprot):CFC21_104703
Chain IDs:L (auth: BO)
Chain Length:151
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6SS17 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):CFC21_074055
Chain IDs:Y (auth: BP)
Chain Length:153
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6LV48 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Gene (Uniprot):CFC21_052703
Chain IDs:Z (auth: BQ)
Chain Length:149
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6HX49 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Chain IDs:M (auth: BR)
Chain Length:143
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B5XY60 Pfam ID:PF00833
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Gene (Uniprot):CFC21_111051
Chain IDs:AA (auth: BS)
Chain Length:152
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6TWW5 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Gene (Uniprot):CFC21_065464, CFC21_076659
Chain IDs:BA (auth: BT)
Chain Length:155
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5FWF5 Pfam ID:PF01090
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S10 domain-containing protein
Chain IDs:CA (auth: BU)
Chain Length:117
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6MKF1 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Gene (Uniprot):CFC21_052197, CFC21_061690
Chain IDs:N (auth: BV)
Chain Length:82
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5EL62 Pfam ID:PF01249
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8, chloroplastic
Gene (Uniprot):CFC21_007684, CFC21_012582, CFC21_042841, CFC21_048691, TRAES_3BF117500090CFD_c1
Chain IDs:O (auth: BW)
Chain Length:130
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:E2F3W4 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Gene (Uniprot):CFC21_036826, CFC21_036828, CFC21_037201, CFC21_042798, CFC21_048659, CFC21_068535, CFC21_080452
Chain IDs:P (auth: BX)
Chain Length:142
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5FV77 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):CFC21_088220, CFC21_088221
Chain IDs:Q (auth: BY)
Chain Length:137
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6PK86 Pfam ID:PF01282
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Gene (Uniprot):CFC21_053846
Chain IDs:GA (auth: BZ)
Chain Length:98
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6HY18 Pfam ID:PF03297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):CFC21_068482, CFC21_068483
Chain IDs:R (auth: Ba)
Chain Length:139
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6KQB8 Pfam ID:PF01283
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Chain IDs:S (auth: Bb)
Chain Length:263
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A341UET3 Pfam ID:PF01667
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):CFC21_038625, CFC21_038626, CFC21_050693, CFC21_052484, CFC21_052485, CFC21_061583
Chain IDs:DA (auth: Bc)
Chain Length:65
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5E8X2 Pfam ID:PF01200
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Gene (Uniprot):CFC21_067854, CFC21_067862, CFC21_067864, CFC21_070567
Chain IDs:EA (auth: Bd)
Chain Length:227
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A1D5ZKM9 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):CFC21_101292
Chain IDs:T (auth: Be)
Chain Length:62
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6S9M7 Pfam ID:PF04758
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitogen-activated protein kinase
Gene (Uniprot):CFC21_008707
Chain IDs:FA (auth: Bg)
Chain Length:250
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B5Z4Q0 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Gene (Uniprot):RPL41
Chain IDs:U (auth: Cn)
Chain Length:25
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:P62124 Pfam ID:PF05162
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
Ligand Molecules
K
MG
ZN
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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
8JIW
Feedback Form
Name
Email
Institute
Feedback