9VTJ | pdb_00009vtj

cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 60S and cycloheximide (CHX)

PDB DOI: https://doi.org/10.2210/pdb9VTJ/pdb
EM Map EMD-65330: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Nicotiana benthamiana, synthetic construct
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: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 60S and cycloheximide (CHX)

Lu, G., Lin, J.

To be published.

Macromolecule Content

Total Structure Weight: 2,060.31 kDa
Atom Count: 129,498
Modeled Residue Count: 10,161
Deposited Residue Count: 10,942
Unique protein chains: 42
Unique nucleic acid chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein	A [auth LA]	217	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3Y379 (Nicotiana tabacum) Explore A0A1S3Y379 Go to UniProtKB: A0A1S3Y379
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1S3Y379
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L8-like	B [auth LB]	260	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3XXQ5 (Nicotiana tabacum) Explore A0A1S3XXQ5 Go to UniProtKB: A0A1S3XXQ5
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UniProt Group	A0A1S3XXQ5
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L3	C [auth LC]	389	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3ZLI9 (Nicotiana tabacum) Explore A0A1S3ZLI9 Go to UniProtKB: A0A1S3ZLI9
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1S3ZLI9
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L4-like	D [auth LD]	405	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S4BWA4 (Nicotiana tabacum) Explore A0A1S4BWA4 Go to UniProtKB: A0A1S4BWA4
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UniProt Group	A0A1S4BWA4
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L11-1	E [auth LE]	181	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3XAW1 (Nicotiana tabacum) Explore A0A1S3XAW1 Go to UniProtKB: A0A1S3XAW1
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UniProt Group	A0A1S3XAW1
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L9-1	F [auth LF]	194	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S4CJ62 (Nicotiana tabacum) Explore A0A1S4CJ62 Go to UniProtKB: A0A1S4CJ62
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UniProt Group	A0A1S4CJ62
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13a-4	G [auth LG]	206	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3Z662 (Nicotiana tabacum) Explore A0A1S3Z662 Go to UniProtKB: A0A1S3Z662
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UniProt Group	A0A1S3Z662
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23	H [auth LH]	140	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3XSQ1 (Nicotiana tabacum) Explore A0A1S3XSQ1 Go to UniProtKB: A0A1S3XSQ1
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UniProt Group	A0A1S3XSQ1
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
60s ribosomal protein l27a-3	I [auth LI]	148	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1J6IJF4 (Nicotiana attenuata) Explore A0A1J6IJF4 Go to UniProtKB: A0A1J6IJF4
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UniProt Group	A0A1J6IJF4
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L10	J [auth LJ]	219	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3Z2D7 (Nicotiana tabacum) Explore A0A1S3Z2D7 Go to UniProtKB: A0A1S3Z2D7
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UniProt Group	A0A1S3Z2D7
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L5-like	K [auth LK]	293	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3XE16 (Nicotiana tabacum) Explore A0A1S3XE16 Go to UniProtKB: A0A1S3XE16
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UniProt Group	A0A1S3XE16
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L17-1 isoform X2	L [auth LL]	175	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S4DQP0 (Nicotiana tabacum) Explore A0A1S4DQP0 Go to UniProtKB: A0A1S4DQP0
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UniProt Group	A0A1S4DQP0
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL23	M [auth LM]	154	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for Q07761 (Nicotiana tabacum) Explore Q07761 Go to UniProtKB: Q07761
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07761
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L26-1	N [auth LN]	146	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S4CC07 (Nicotiana tabacum) Explore A0A1S4CC07 Go to UniProtKB: A0A1S4CC07
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1S4CC07
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35-like	O [auth LO]	123	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3WY31 (Nicotiana tabacum) Explore A0A1S3WY31 Go to UniProtKB: A0A1S3WY31
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UniProt Group	A0A1S3WY31
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7-4-like	P [auth LP]	242	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1U7X2X8 (Nicotiana sylvestris) Explore A0A1U7X2X8 Go to UniProtKB: A0A1U7X2X8
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UniProt Group	A0A1U7X2X8
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L6-like isoform X1	Q [auth LQ]	230	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1U7WD54 (Nicotiana sylvestris) Explore A0A1U7WD54 Go to UniProtKB: A0A1U7WD54
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UniProt Group	A0A1U7WD54
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7a	R [auth LR]	237	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1U7XNI3 (Nicotiana sylvestris) Explore A0A1U7XNI3 Go to UniProtKB: A0A1U7XNI3
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UniProt Group	A0A1U7XNI3
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13	S [auth LS]	200	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S4CSN1 (Nicotiana tabacum) Explore A0A1S4CSN1 Go to UniProtKB: A0A1S4CSN1
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UniProt Group	A0A1S4CSN1
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L14-1	T [auth LT]	130	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1U7UYX7 (Nicotiana sylvestris) Explore A0A1U7UYX7 Go to UniProtKB: A0A1U7UYX7
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UniProt Group	A0A1U7UYX7
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L15	U [auth LU]	204	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3XIA7 (Nicotiana tabacum) Explore A0A1S3XIA7 Go to UniProtKB: A0A1S3XIA7
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UniProt Group	A0A1S3XIA7
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18-2	V [auth LV]	187	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S4DF55 (Nicotiana tabacum) Explore A0A1S4DF55 Go to UniProtKB: A0A1S4DF55
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UniProt Group	A0A1S4DF55
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L19	W [auth LW]	211	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S4A7M5 (Nicotiana tabacum) Explore A0A1S4A7M5 Go to UniProtKB: A0A1S4A7M5
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UniProt Group	A0A1S4A7M5
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18a	X [auth LX]	178	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1U7V5H1 (Nicotiana sylvestris) Explore A0A1U7V5H1 Go to UniProtKB: A0A1U7V5H1
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UniProt Group	A0A1U7V5H1
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L21-1-like	Y [auth LY]	164	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3XCW6 (Nicotiana tabacum) Explore A0A1S3XCW6 Go to UniProtKB: A0A1S3XCW6
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UniProt Group	A0A1S3XCW6
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL22	Z [auth LZ]	108	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S4BSU3 (Nicotiana tabacum) Explore A0A1S4BSU3 Go to UniProtKB: A0A1S4BSU3
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UniProt Group	A0A1S4BSU3
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L24	AA [auth La]	164	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S4BHF2 (Nicotiana tabacum) Explore A0A1S4BHF2 Go to UniProtKB: A0A1S4BHF2
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UniProt Group	A0A1S4BHF2
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27	BA [auth Lb]	135	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3XBV7 (Nicotiana tabacum) Explore A0A1S3XBV7 Go to UniProtKB: A0A1S3XBV7
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UniProt Group	A0A1S3XBV7
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L28-1-like	CA [auth Lc]	143	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1U7WYY1 (Nicotiana sylvestris) Explore A0A1U7WYY1 Go to UniProtKB: A0A1U7WYY1
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UniProt Group	A0A1U7WYY1
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L29	DA [auth Ld]	50	Nicotiana benthamiana	Mutation(s): 0

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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L30	EA [auth Le]	113	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3WZ09 (Nicotiana tabacum) Explore A0A1S3WZ09 Go to UniProtKB: A0A1S3WZ09
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UniProt Group	A0A1S3WZ09
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L31	FA [auth Lf]	120	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S3Y3V5 (Nicotiana tabacum) Explore A0A1S3Y3V5 Go to UniProtKB: A0A1S3Y3V5
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UniProt Group	A0A1S3Y3V5
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L32-1	GA [auth Lg]	133	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1U7YAK1 (Nicotiana sylvestris) Explore A0A1U7YAK1 Go to UniProtKB: A0A1U7YAK1
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UniProt Group	A0A1U7YAK1
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35a-3-like	HA [auth Lh]	112	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S4AHL7 (Nicotiana tabacum) Explore A0A1S4AHL7 Go to UniProtKB: A0A1S4AHL7
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UniProt Group	A0A1S4AHL7
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL34	IA [auth Li]	120	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for P41098 (Nicotiana tabacum) Explore P41098 Go to UniProtKB: P41098
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UniProt Group	P41098
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L36	JA [auth Lj]	110	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1U7VXX3 (Nicotiana sylvestris) Explore A0A1U7VXX3 Go to UniProtKB: A0A1U7VXX3
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UniProt Group	A0A1U7VXX3
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L37	KA [auth Lk]	95	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S4DN51 (Nicotiana tabacum) Explore A0A1S4DN51 Go to UniProtKB: A0A1S4DN51
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UniProt Group	A0A1S4DN51
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L38	LA [auth Ll]	69	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1S4C4G8 (Nicotiana tabacum) Explore A0A1S4C4G8 Go to UniProtKB: A0A1S4C4G8
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UniProt Group	A0A1S4C4G8
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L39-3	MA [auth Lm]	51	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1U7Y1K3 (Nicotiana sylvestris) Explore A0A1U7Y1K3 Go to UniProtKB: A0A1U7Y1K3
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UniProt Group	A0A1U7Y1K3
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-60S ribosomal protein L40	NA [auth Ln]	128	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1U7X7W2 (Nicotiana sylvestris) Explore A0A1U7X7W2 Go to UniProtKB: A0A1U7X7W2
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UniProt Group	A0A1U7X7W2
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L44	OA [auth Lp]	105	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1U7YPT7 (Nicotiana sylvestris) Explore A0A1U7YPT7 Go to UniProtKB: A0A1U7YPT7
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UniProt Group	A0A1U7YPT7
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L37a	PA [auth Lq]	77	Nicotiana benthamiana	Mutation(s): 0
UniProt
Find proteins for A0A1U7XSD1 (Nicotiana sylvestris) Explore A0A1U7XSD1 Go to UniProtKB: A0A1U7XSD1
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UniProt Group	A0A1U7XSD1
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Molecule	Chains	Length	Organism
Entity ID: 43
RNA (204-MER)	QA [auth 10]	204	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 44
5S rRNA	RA [auth 12]	119	Nicotiana benthamiana
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Molecule	Chains	Length	Organism
Entity ID: 45
5.8S rRNA	SA [auth 13]	163	Nicotiana benthamiana
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Molecule	Chains	Length	Organism
Entity ID: 46
25S rRNA	TA [auth 14]	3,390	Nicotiana benthamiana
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Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-15

Deposition Author(s):

Lu, G.

Lin, J.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32130063
National Natural Science Foundation of China (NSFC)	China	32471349

Revision History (Full details and data files)

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

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9VTJ | pdb_00009vtj

cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 60S and cycloheximide (CHX)

Literature

cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 60S and cycloheximide (CHX)

Biological Assembly 1

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