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:
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 L13)
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 L14)
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 L15)
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 L18)
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 L19)
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 L18a)
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 L21)
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 L22)
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 L24)
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 L27)
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 L28)
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 L29)
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 L30)
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 L31)
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 L32)
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 L35a)
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 L34)
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 L36)
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 L37)
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 L38)
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 L39)
Gene (Uniprot):LOC107778797
Chain IDs:V (auth: X)
Chain Length:51
Number of Molecules:1
Biological Source:Nicotiana tabacum
Polymer Type:polypeptide(L)
Molecule:eL40 (60S ribosomal protein L40)
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 L42)
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 L37a)
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 L7a)
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 L13a)
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 L23)
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 L27a)
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 L10)
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 L5)
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 L17)
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 L23a)
Gene (Uniprot):RPL23A
Chain IDs:IA (auth: k)
Chain Length:154
Number of Molecules:1
Biological Source:Nicotiana tabacum
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 L26)
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 L35)
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 L41)
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 L7)
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 L11)
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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Disease

Primary Citation of related structures