8AZW image
Deposition Date 2022-09-06
Release Date 2023-06-07
Last Version Date 2024-07-24
Entry Detail
PDB ID:
8AZW
Keywords:
Title:
Cryo-EM structure of the plant 60S subunit
Biological Source:
Source Organism(s):
Method Details:
Experimental Method:
Resolution:
2.14 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:SA (auth: A)
Chain Length:3390
Number of Molecules:1
Biological Source:Nicotiana tabacum
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:TA (auth: B)
Chain Length:163
Number of Molecules:1
Biological Source:Nicotiana tabacum
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:A (auth: C)
Chain Length:119
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL13 (60S ribosomal protein L
Gene (Uniprot):LOC107822051
Chain IDs:B (auth: D)
Chain Length:206
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL14 (60S ribosomal protein L
Gene (Uniprot):LOC107794709
Chain IDs:C (auth: E)
Chain Length:134
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL15 (60S ribosomal protein L
Gene (Uniprot):LOC107826284
Chain IDs:D (auth: F)
Chain Length:204
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL18 (60S ribosomal protein L
Gene (Uniprot):LOC107829149
Chain IDs:E (auth: G)
Chain Length:187
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL19 (60S ribosomal protein L
Gene (Uniprot):LOC107759916
Chain IDs:F (auth: H)
Chain Length:214
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL20 (60S ribosomal protein L
Gene (Uniprot):LOC107820975
Chain IDs:G (auth: I)
Chain Length:178
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL21 (60S ribosomal protein L
Gene (Uniprot):LOC107763612
Chain IDs:H (auth: J)
Chain Length:175
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL22 (60S ribosomal protein L
Gene (Uniprot):LOC107811461
Chain IDs:I (auth: K)
Chain Length:154
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL24 (60S ribosomal protein L
Gene (Uniprot):LOC107808292
Chain IDs:J (auth: L)
Chain Length:24
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL27 (60S ribosomal protein L
Gene (Uniprot):LOC107796761
Chain IDs:K (auth: M)
Chain Length:135
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL28 (60S ribosomal protein L
Gene (Uniprot):LOC107824985
Chain IDs:L (auth: N)
Chain Length:123
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL29 (60S ribosomal protein L
Gene (Uniprot):LOC107778781
Chain IDs:M (auth: O)
Chain Length:61
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL30 (60S ribosomal protein L
Gene (Uniprot):LOC107759448
Chain IDs:N (auth: P)
Chain Length:25
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL31 (60S ribosomal protein L
Gene (Uniprot):LOC107771890
Chain IDs:O (auth: Q)
Chain Length:120
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL32 (60S ribosomal protein L
Gene (Uniprot):LOC107782359
Chain IDs:P (auth: R)
Chain Length:133
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL33 (60S ribosomal protein L
Gene (Uniprot):LOC107768641
Chain IDs:Q (auth: S)
Chain Length:405
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL34 (60S ribosomal protein L
Gene (Uniprot):RPL34
Chain IDs:R (auth: T)
Chain Length:181
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL36 (60S ribosomal protein L
Gene (Uniprot):LOC107825165
Chain IDs:S (auth: U)
Chain Length:110
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL37 (60S ribosomal protein L
Gene (Uniprot):LOC107831585
Chain IDs:T (auth: V)
Chain Length:95
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL38 (60S ribosomal protein L
Gene (Uniprot):LOC107815038
Chain IDs:U (auth: W)
Chain Length:69
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL39 (60S ribosomal protein L
Gene (Uniprot):LOC107778797
Chain IDs:V (auth: X)
Chain Length:51
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL40 (60S ribosomal protein L
Chain IDs:W (auth: Y)
Chain Length:128
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL42 (60S ribosomal protein L
Gene (Uniprot):LOC107801799
Chain IDs:Y (auth: Z)
Chain Length:105
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL43 (60S ribosomal protein L
Gene (Uniprot):LOC107761416
Chain IDs:Z (auth: a)
Chain Length:3390
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL6 (60S ribosomal protein L6
Gene (Uniprot):LOC107803255
Chain IDs:AA (auth: b)
Chain Length:163
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL8 (60S ribosomal protein L7
Gene (Uniprot):LOC107826327
Chain IDs:BA (auth: c)
Chain Length:119
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL13 (60S ribosomal protein L
Gene (Uniprot):LOC107831576
Chain IDs:CA (auth: d)
Chain Length:206
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL14 (60S ribosomal protein L
Gene (Uniprot):LOC107768301
Chain IDs:DA (auth: e)
Chain Length:134
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL15 (60S ribosomal protein L
Gene (Uniprot):LOC107807693
Chain IDs:EA (auth: f)
Chain Length:204
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL16 (60S ribosomal protein L
Gene (Uniprot):LOC107782233
Chain IDs:FA (auth: g)
Chain Length:187
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL18 (60S ribosomal protein L
Gene (Uniprot):LOC107764090
Chain IDs:GA (auth: h)
Chain Length:214
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL22 (60S ribosomal protein L
Gene (Uniprot):LOC107817504
Chain IDs:HA (auth: j)
Chain Length:175
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL23 (60S ribosomal protein L
Gene (Uniprot):RPL23A
Chain IDs:IA (auth: k)
Chain Length:154
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:nascent chain
Chain IDs:RA (auth: l)
Chain Length:24
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL24 (60S ribosomal protein L
Gene (Uniprot):LOC107831809
Chain IDs:JA (auth: m)
Chain Length:135
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL29 (60S ribosomal protein L
Gene (Uniprot):LOC107759229
Chain IDs:KA (auth: n)
Chain Length:123
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL2 (60S ribosomal protein L8
Gene (Uniprot):LOC107769978
Chain IDs:LA (auth: o)
Chain Length:61
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL41 (60S ribosomal protein L
Gene (Uniprot):RPL41
Chain IDs:X (auth: p)
Chain Length:25
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL30 (60S ribosomal protein L
Gene (Uniprot):LOC107794124
Chain IDs:MA (auth: q)
Chain Length:120
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL3 (60S ribosomal protein L3
Gene (Uniprot):LOC107788247
Chain IDs:NA (auth: r)
Chain Length:133
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL4 (60S ribosomal protein L4
Gene (Uniprot):LOC107759872
Chain IDs:OA (auth: s)
Chain Length:405
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL5 (60S ribosomal protein L1
Gene (Uniprot):LOC107763118
Chain IDs:PA (auth: t)
Chain Length:181
Number of Molecules:1
Biological Source:Nicotiana tabacum
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uL6 (60S ribosomal protein L9
Gene (Uniprot):LOC107813756
Chain IDs:QA (auth: u)
Chain Length:110
Number of Molecules:1
Biological Source:Nicotiana tabacum
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
A2M TA A modified residue
OMG TA G modified residue
PSU TA U modified residue
Primary Citation
Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution.
Nat.Plants 9 987 1000 (2023)
PMID: 37156858 DOI: 10.1038/s41477-023-01407-y

Abstact

In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 Å. The ribosome structure includes two tRNAs, decoded mRNA and the nascent peptide chain, thus providing insights into the molecular underpinnings of the cytosolic translation process in plants. The map displays conserved and plant-specific rRNA modifications and the positions of numerous ionic cofactors, and it uncovers the role of monovalent ions in the decoding centre. The model of the plant 80S ribosome enables broad phylogenetic comparisons that reveal commonalities and differences in the ribosomes of plants and those of other eukaryotes, thus putting our knowledge about eukaryotic translation on a firmer footing.

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Primary Citation of related structures
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