ISDA

Entry Detail

PDB ID:

8JIV

EMDB ID:

EMD-36331

Keywords:

RIBOSOME

Title:

Atomic structure of wheat ribosome reveals unique features of the plant ribosomes

Biological Source:

Source Organism:

Triticum aestivum

PDB Version:

Deposition Date:

2023-05-28

Release Date:

2024-03-27

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.84 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Description:25S rRNA
Chain IDs:A (auth: Aa)
Chain Length:3391
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:B (auth: Ab)
Chain Length:119
Number of Molecules:1
Biological Source:Triticum aestivum

Polymer Type:polyribonucleotide
Description:5.8S rRNA
Chain IDs:C (auth: Ac)
Chain Length:158
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Description:Ribosomal protein L2 C-terminal domain-containing protein
Chain IDs:D (auth: CA)
Chain Length:261
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:W5ECL2 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Description:Ribosomal protein L3
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)
Description: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

Protein Blast

Polymer Type:polypeptide(L)
Description:Ribosomal protein L5 eukaryotic C-terminal domain-containing protein
Chain IDs:G (auth: CD)
Chain Length:307
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A3B6DD91 Pfam ID:PF17144, PF14204

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6
Chain IDs:H (auth: CE)
Chain Length:232
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A3B6QGW3 Pfam ID:PF01159

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein uL30
Chain IDs:I (auth: CF)
Chain Length:111
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A3B6DM38 Pfam ID:PF08079, PF00327

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7a
Chain IDs:J (auth: CG)
Chain Length:258
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A3B6RED0 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Description: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

Protein Blast

Polymer Type:polypeptide(L)
Description:Ribosomal protein L10e/L16 domain-containing protein
Chain IDs:L (auth: CI)
Chain Length:111
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A3B6HUM3 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Description: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

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13
Chain IDs:N (auth: CL)
Chain Length:208
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A3B6QBU0 Pfam ID:PF01294

Protein Blast

Polymer Type:polypeptide(L)
Description:Ribosomal protein L14e domain-containing protein
Chain IDs:O (auth: CM)
Chain Length:135
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A3B6DGT8 Pfam ID:PF01929

Protein Blast

Polymer Type:polypeptide(L)
Description:Ribosomal protein L15
Chain IDs:P (auth: CN)
Chain Length:204
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:W5FEX7 Pfam ID:PF00827

Protein Blast

Polymer Type:polypeptide(L)
Description:Ribosomal protein L13a
Chain IDs:Q (auth: CO)
Chain Length:206
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7L1 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein uL22
Chain IDs:R (auth: CP)
Chain Length:170
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:W5FSM8 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Description: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

Protein Blast

Polymer Type:polypeptide(L)
Description:Ribosomal protein L19
Chain IDs:T (auth: CR)
Chain Length:206
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A3B6C2W3 Pfam ID:PF01280

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18a
Chain IDs:U (auth: CS)
Chain Length:178
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A3B5Z5M6 Pfam ID:PF01775

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21
Chain IDs:V (auth: CT)
Chain Length:164
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A9R1HBE9

Protein Blast

Polymer Type:polypeptide(L)
Description:Genome assembly, chromosome: II
Chain IDs:W (auth: CU)
Chain Length:129
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:W5C5N9 Pfam ID:PF01776

Protein Blast

Polymer Type:polypeptide(L)
Description:Ribosomal protein L17
Chain IDs:X (auth: CV)
Chain Length:136
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K4 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Description:TRASH domain-containing protein
Chain IDs:Y (auth: CW)
Chain Length:161
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A3B6ELC9 Pfam ID:PF01246

Protein Blast

Polymer Type:polypeptide(L)
Description:Genome assembly, chromosome: II
Chain IDs:Z (auth: CX)
Chain Length:152
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A1D5UQZ5 Pfam ID:PF03939, PF00276

Protein Blast

Polymer Type:polypeptide(L)
Description: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

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27
Chain IDs:BA (auth: CZ)
Chain Length:137
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A341XZK6 Pfam ID:PF00467, PF01777

Protein Blast

Polymer Type:polypeptide(L)
Description: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

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:DA (auth: Cb)
Chain Length:60
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A1D5RRD3 Pfam ID:PF01779

Protein Blast

Polymer Type:polypeptide(L)
Description: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

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31
Chain IDs:FA (auth: Cd)
Chain Length:307
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:W5G990 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein eL32
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)
Description:60S ribosomal protein eL33
Chain IDs:HA (auth: Cf)
Chain Length:111
Number of Molecules:1
Biological Source:Triticum aestivum

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34
Chain IDs:IA (auth: Cg)
Chain Length:258
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A3B6RFY8 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35
Chain IDs:JA (auth: Ch)
Chain Length:124
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q8L805 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36
Chain IDs:KA (auth: Ci)
Chain Length:111
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A1D5S805 Pfam ID:PF01158

Protein Blast

Polymer Type:polypeptide(L)
Description:Ribosomal protein L37
Chain IDs:LA (auth: Cj)
Chain Length:93
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A1D6BC85 Pfam ID:PF01907

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:MA (auth: Ck)
Chain Length:69
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A1D5W6Q2 Pfam ID:PF01781

Protein Blast

Polymer Type:polypeptide(L)
Description:Ribosomal protein L39
Chain IDs:NA (auth: Cl)
Chain Length:208
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:Q5I7K7 Pfam ID:PF00832

Protein Blast

Polymer Type:polypeptide(L)
Description:Ubiquitin-like domain-containing protein
Chain IDs:OA (auth: Cm)
Chain Length:135
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:A0A1D5XNC2 Pfam ID:PF00240, PF01020

Protein Blast

Polymer Type:polypeptide(L)
Description: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

Protein Blast

Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37a, expressed
Chain IDs:QA (auth: Cp)
Chain Length:170
Number of Molecules:1
Biological Source:Triticum aestivum

UniProt ID:D8L9P6 Pfam ID:PF01780

Protein Blast

Polymer Type:polypeptide(L)
Description: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
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

Primary Citation

Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes.

Mishra, R.K, Sharma, P, Khaja, F.T, Uday, A.B, Hussain, T, Uday, A.B, Khaja, F.T.Show

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