8JIV image
Deposition Date 2023-05-28
Release Date 2024-03-27
Last Version Date 2024-05-22
Entry Detail
PDB ID:
8JIV
Keywords:
RIBOSOME
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:
2.84 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8JIV validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:A (auth: Aa)
Chain Length:3391
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B (auth: Ab)
Chain Length:119
Number of Molecules:1
Biological Source:Triticum aestivum
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:C (auth: Ac)
Chain Length:158
Number of Molecules:1
Biological Source:Triticum aestivum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L2 C-terminal domain-containing protein
Gene (Uniprot):CFC21_052694, CFC21_057232, CFC21_061205, CFC21_064588, CFC21_070369, CFC21_076331
Chain IDs:D (auth: CA)
Chain Length:261
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5ECL2 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L3
Gene (Uniprot):LOC123120076
Chain IDs:E (auth: CB)
Chain Length:60
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:Q7X744 Pfam ID:PF00297
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4 C-terminal domain-containing protein
Chain IDs:F (auth: CC)
Chain Length:405
Number of Molecules:1
Biological Source:Triticum aestivum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L5 eukaryotic C-terminal domain-containing protein
Gene (Uniprot):CFC21_030053
Chain IDs:G (auth: CD)
Chain Length:307
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6DD91 Pfam ID:PF17144, PF14204
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):CFC21_092553
Chain IDs:H (auth: CE)
Chain Length:232
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6QGW3 Pfam ID:PF01159
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL30
Gene (Uniprot):CFC21_075603
Chain IDs:I (auth: CF)
Chain Length:111
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6DM38 Pfam ID:PF08079, PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Gene (Uniprot):CFC21_097640
Chain IDs:J (auth: CG)
Chain Length:258
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6RED0 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L6 alpha-beta domain-containing protein
Chain IDs:K (auth: CH)
Chain Length:124
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A9R1FDI5
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L10e/L16 domain-containing protein
Gene (Uniprot):CFC21_052842
Chain IDs:L (auth: CI)
Chain Length:111
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6HUM3 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Chain IDs:M (auth: CJ)
Chain Length:93
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B5XX39 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Gene (Uniprot):CFC21_091236
Chain IDs:N (auth: CL)
Chain Length:208
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6QBU0 Pfam ID:PF01294
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L14e domain-containing protein
Gene (Uniprot):CFC21_030928
Chain IDs:O (auth: CM)
Chain Length:135
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6DGT8 Pfam ID:PF01929
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Gene (Uniprot):CAMPLR22A2D_LOCUS2234, CFC21_029414, CFC21_065333, CFC21_077061
Chain IDs:P (auth: CN)
Chain Length:204
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5FEX7 Pfam ID:PF00827
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L13a
Gene (Uniprot):LOC606336
Chain IDs:Q (auth: CO)
Chain Length:206
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:Q5I7L1 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL22
Gene (Uniprot):CFC21_071208, CFC21_077189
Chain IDs:R (auth: CP)
Chain Length:170
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5FSM8 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L18e/L15P domain-containing protein
Chain IDs:S (auth: CQ)
Chain Length:188
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B5ZQE8 Pfam ID:PF17135
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L19
Gene (Uniprot):CFC21_021776
Chain IDs:T (auth: CR)
Chain Length:206
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6C2W3 Pfam ID:PF01280
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):CFC21_009020
Chain IDs:U (auth: CS)
Chain Length:178
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B5Z5M6 Pfam ID:PF01775
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Chain IDs:V (auth: CT)
Chain Length:164
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A9R1HBE9
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Genome assembly, chromosome: II
Gene (Uniprot):CAMPLR22A2D_LOCUS969, CFC21_028134
Chain IDs:W (auth: CU)
Chain Length:129
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5C5N9 Pfam ID:PF01776
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L17
Gene (Uniprot):LOC123180988
Chain IDs:X (auth: CV)
Chain Length:136
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:Q5I7K4 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:TRASH domain-containing protein
Gene (Uniprot):CFC21_036687
Chain IDs:Y (auth: CW)
Chain Length:161
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6ELC9 Pfam ID:PF01246
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Genome assembly, chromosome: II
Gene (Uniprot):CAMPLR22A2D_LOCUS3567, CFC21_010645, CFC21_024362, CFC21_030666
Chain IDs:Z (auth: CX)
Chain Length:152
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A1D5UQZ5 Pfam ID:PF03939, PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:KOW domain-containing protein
Chain IDs:AA (auth: CY)
Chain Length:127
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5D739 Pfam ID:PF16906, PF00467
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):CFC21_098384
Chain IDs:BA (auth: CZ)
Chain Length:137
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A341XZK6 Pfam ID:PF00467, PF01777
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L18e/L15P domain-containing protein
Chain IDs:CA (auth: Ca)
Chain Length:261
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6AUW8 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):CFC21_007097, CFC21_011996
Chain IDs:DA (auth: Cb)
Chain Length:60
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A1D5RRD3 Pfam ID:PF01779
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L7Ae/L30e/S12e/Gadd45 domain-containing protein
Chain IDs:EA (auth: Cc)
Chain Length:405
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:Q5I7K9 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Gene (Uniprot):CFC21_084218, CFC21_093418
Chain IDs:FA (auth: Cd)
Chain Length:307
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:W5G990 Pfam ID:PF01198
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL32
Gene (Uniprot):CFC21_102549
Chain IDs:GA (auth: Ce)
Chain Length:232
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6SDD9 Pfam ID:PF01655
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL33
Chain IDs:HA (auth: Cf)
Chain Length:111
Number of Molecules:1
Biological Source:Triticum aestivum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34
Gene (Uniprot):CFC21_098055
Chain IDs:IA (auth: Cg)
Chain Length:258
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6RFY8 Pfam ID:PF01199
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):RPL35
Chain IDs:JA (auth: Ch)
Chain Length:124
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:Q8L805 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):CFC21_007670, CFC21_007673, CFC21_012565
Chain IDs:KA (auth: Ci)
Chain Length:111
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A1D5S805 Pfam ID:PF01158
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Gene (Uniprot):CFC21_086135, CFC21_091005, CFC21_091010
Chain IDs:LA (auth: Cj)
Chain Length:93
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A1D6BC85 Pfam ID:PF01907
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):CFC21_043473, CFC21_044750
Chain IDs:MA (auth: Ck)
Chain Length:69
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A1D5W6Q2 Pfam ID:PF01781
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L39
Gene (Uniprot):LOC123150917
Chain IDs:NA (auth: Cl)
Chain Length:208
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:Q5I7K7 Pfam ID:PF00832
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-like domain-containing protein
Gene (Uniprot):CFC21_051579, CFC21_053842, CFC21_056000, CFC21_060038, CFC21_062406
Chain IDs:OA (auth: Cm)
Chain Length:135
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A1D5XNC2 Pfam ID:PF00240, PF01020
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Genome assembly, chromosome: II
Chain IDs:PA (auth: Co)
Chain Length:206
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B6C6X2 Pfam ID:PF00935
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a, expressed
Gene (Uniprot):LOC123183015
Chain IDs:QA (auth: Cp)
Chain Length:170
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:D8L9P6 Pfam ID:PF01780
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal L28e/Mak16 domain-containing protein
Chain IDs:RA (auth: Cr)
Chain Length:206
Number of Molecules:1
Biological Source:Triticum aestivum
UniProt ID:A0A3B5Y651 Pfam ID:PF01778
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MA A A modified residue
5MC A C modified residue
A2M A A modified residue
HIC E HIS modified residue
MLZ PA LYS modified residue
OMC A C modified residue
OMG A G modified residue
OMU A U modified residue
PSU A U modified residue
UR3 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
8JIV