9VTI | pdb_00009vti

cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S

  • Classification: RIBOSOME
  • Organism(s): Nicotiana benthamiana
  • Mutation(s): No 

  • Deposited: 2025-07-10 Released: 2026-07-15 
  • Deposition Author(s): Lu, G., Lin, J.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.0 of the entry. See complete history

Literature

cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S

Lu, G.Lin, J.

To be published.

Macromolecule Content 

  • Total Structure Weight: 3,214.15 kDa 
  • Atom Count: 199,397 
  • Modeled Residue Count: 16,198 
  • Deposited Residue Count: 17,789 
  • Unique protein chains: 75
  • Unique nucleic acid chains: 5

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2A [auth SA]257Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1U7W513 (Nicotiana sylvestris)
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S3, chloroplasticB [auth SB]248Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1U7WQT4 (Nicotiana sylvestris)
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-2-likeC [auth SC]187Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1U7X6K6 (Nicotiana sylvestris)
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5D [auth SD]280Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1U7Y544 (Nicotiana sylvestris)
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S5E [auth SE]210Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4AYA1 (Nicotiana tabacum)
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8cF [auth SF]130Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1U7YEG5 (Nicotiana sylvestris)
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S16G [auth SG]147Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4AU23 (Nicotiana tabacum)
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S20-2H [auth SH]122Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3XHL0 (Nicotiana tabacum)
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-2I [auth SI]150Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1U7X6S8 (Nicotiana sylvestris)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S23J [auth SJ]142Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1U7W217 (Nicotiana sylvestris)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S18K [auth SK]141Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4AJE0 (Nicotiana tabacum)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S29L [auth SL]56Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1U7V0A7 (Nicotiana sylvestris)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S13M [auth SM]151Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3ZRI7 (Nicotiana tabacum)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S11N [auth SN]159Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4BW10 (Nicotiana tabacum)
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S15-likeO [auth SO]152Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1U7X1Z5 (Nicotiana sylvestris)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1P [auth SP]261Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for Q285L8 (Nicotiana tabacum)
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S4Q [auth SQ]264Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4DQ51 (Nicotiana tabacum)
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S6R [auth SR]249Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3Z3Y7 (Nicotiana tabacum)
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S7S [auth SS]191Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3Z906 (Nicotiana tabacum)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S8T [auth ST]212Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4CZK3 (Nicotiana tabacum)
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-1U [auth SU]118Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4DHU6 (Nicotiana tabacum)
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S12V [auth SV]143Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4BEE0 (Nicotiana tabacum)
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-likeW [auth SW]131Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3Z9G2 (Nicotiana tabacum)
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-3-likeX [auth SX]143Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4CYT7 (Nicotiana tabacum)
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S21Y [auth SY]82Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4C2G0 (Nicotiana tabacum)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S24Z [auth SZ]133Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3ZXI6 (Nicotiana tabacum)
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S25AA [auth Sa]74Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1U7UZX1 (Nicotiana sylvestris)
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S26BA [auth Sb]113Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4A5C8 (Nicotiana tabacum)
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S27CA [auth Sc]85Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4BH20 (Nicotiana tabacum)
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S28DA [auth Sd]65Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1U7VNF8 (Nicotiana sylvestris)
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S30EA [auth Se]62Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3XGJ0 (Nicotiana tabacum)
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27a-likeFA [auth Sf]156Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1U7WCX2 (Nicotiana sylvestris)
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal proteinGA [auth LA]217Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3Y379 (Nicotiana tabacum)
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-likeHA [auth LB]260Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3XXQ5 (Nicotiana tabacum)
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L3IA [auth LC]389Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3ZLI9 (Nicotiana tabacum)
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-likeJA [auth LD]405Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4BWA4 (Nicotiana tabacum)
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-1KA [auth LE]181Nicotiana benthamianaMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-1LA [auth LF]194Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4CJ62 (Nicotiana tabacum)
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L13a-4MA [auth LG]206Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3Z662 (Nicotiana tabacum)
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L23NA [auth LH]140Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3XSQ1 (Nicotiana tabacum)
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
60s ribosomal protein l27a-3OA [auth LI]148Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1J6IJF4 (Nicotiana attenuata)
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L10PA [auth LJ]219Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3Z2D7 (Nicotiana tabacum)
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L5-likeQA [auth LK]293Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S3XE16 (Nicotiana tabacum)
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-1 isoform X2RA [auth LL]175Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for A0A1S4DQP0 (Nicotiana tabacum)
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23SA [auth LM]154Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for Q07761 (Nicotiana tabacum)
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-1TA [auth LN]146Nicotiana benthamianaMutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-likeUA [auth LO]123Nicotiana benthamianaMutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-4-likeVA [auth LP]242Nicotiana benthamianaMutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-like isoform X1WA [auth LQ]230Nicotiana benthamianaMutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aXA [auth LR]237Nicotiana benthamianaMutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L13YA [auth LS]200Nicotiana benthamianaMutation(s): 0 
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-1ZA [auth LT]130Nicotiana benthamianaMutation(s): 0 
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L15AB [auth LU]204Nicotiana benthamianaMutation(s): 0 
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-2BB [auth LV]187Nicotiana benthamianaMutation(s): 0 
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Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L19CB [auth LW]211Nicotiana benthamianaMutation(s): 0 
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Entity ID: 56
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aDB [auth LX]178Nicotiana benthamianaMutation(s): 0 
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Entity ID: 57
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-1-likeEB [auth LY]164Nicotiana benthamianaMutation(s): 0 
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Find proteins for A0A1S3XCW6 (Nicotiana tabacum)
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Entity ID: 58
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22FB [auth LZ]108Nicotiana benthamianaMutation(s): 0 
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Entity ID: 59
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L24GB [auth La]164Nicotiana benthamianaMutation(s): 0 
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Entity ID: 60
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L27HB [auth Lb]135Nicotiana benthamianaMutation(s): 0 
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Entity ID: 61
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L28-1-likeIB [auth Lc]143Nicotiana benthamianaMutation(s): 0 
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Entity ID: 62
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L29JB [auth Ld]50Nicotiana benthamianaMutation(s): 0 
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Entity ID: 63
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L30KB [auth Le]113Nicotiana benthamianaMutation(s): 0 
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Find proteins for A0A1S3WZ09 (Nicotiana tabacum)
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Entity ID: 64
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L31LB [auth Lf]120Nicotiana benthamianaMutation(s): 0 
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Entity ID: 65
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L32-1MB [auth Lg]133Nicotiana benthamianaMutation(s): 0 
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Entity ID: 66
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L35a-3-likeNB [auth Lh]112Nicotiana benthamianaMutation(s): 0 
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Entity ID: 67
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34OB [auth Li]120Nicotiana benthamianaMutation(s): 0 
UniProt
Find proteins for P41098 (Nicotiana tabacum)
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Entity ID: 68
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L36PB [auth Lj]110Nicotiana benthamianaMutation(s): 0 
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Entity ID: 69
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L37QB [auth Lk]95Nicotiana benthamianaMutation(s): 0 
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Entity ID: 70
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L38RB [auth Ll]69Nicotiana benthamianaMutation(s): 0 
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Entity ID: 71
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L39-3SB [auth Lm]51Nicotiana benthamianaMutation(s): 0 
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Entity ID: 72
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40TB [auth Ln]128Nicotiana benthamianaMutation(s): 0 
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Entity ID: 73
MoleculeChains  Sequence LengthOrganismDetailsImage
60s ribosomal protein l41-likeUB [auth Lo]25Nicotiana benthamianaMutation(s): 0 
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Entity ID: 74
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L44VB [auth Lp]105Nicotiana benthamianaMutation(s): 0 
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Entity ID: 75
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aWB [auth Lq]77Nicotiana benthamianaMutation(s): 0 
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Entity ID: 76
MoleculeChains LengthOrganismImage
25S rRNAXB [auth 10]204Nicotiana benthamiana
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Entity ID: 77
MoleculeChains LengthOrganismImage
18S rRNAYB [auth 11]1,808Nicotiana benthamiana
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Entity ID: 78
MoleculeChains LengthOrganismImage
5S rRNAZB [auth 12]119Nicotiana benthamiana
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Entity ID: 79
MoleculeChains LengthOrganismImage
5.8S rRNAAC [auth 13]163Nicotiana benthamiana
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Entity ID: 80
MoleculeChains LengthOrganismImage
25S rRNABC [auth 14]3,390Nicotiana benthamiana
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
CC [auth 10]
DC [auth 10]
EC [auth 10]
FC [auth 10]
GC [auth 10]
CC [auth 10],
DC [auth 10],
EC [auth 10],
FC [auth 10],
GC [auth 10],
HC [auth 10],
IC [auth 10],
JC [auth 14],
KC [auth 14]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2026-07-15 
  • Deposition Author(s): Lu, G., Lin, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32130063
National Natural Science Foundation of China (NSFC)China32471349

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-15
    Type: Initial release