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- PDB-9vti: cryoEM structure of tobacco mosaic virus tRNA-like structure comp... -

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Basic information

Entry
Database: PDB / ID: 9vti
TitlecryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S
Components
  • (25S rRNA) x 2
  • (40S ribosomal protein ...) x 26
  • (60S ribosomal protein ...) x 35
  • (Large ribosomal subunit protein ...) x 3
  • (Ribosomal protein ...) x 3
  • (Small ribosomal subunit protein ...) x 4
  • 18S rRNA
  • 30S ribosomal protein S3, chloroplastic
  • 5.8S rRNA
  • 5S rRNA
  • Ribosomal protein
  • Ubiquitin-40S ribosomal protein S27a-like
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / tRNA-like structure / tobacco / Nicotiana benthamiana / tobacco mosaic virus / RNA structure / translation
Function / homology
Function and homology information


adaxial/abaxial pattern specification / leaf morphogenesis / response to high light intensity / response to UV-B / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...adaxial/abaxial pattern specification / leaf morphogenesis / response to high light intensity / response to UV-B / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / rRNA processing / ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. ...Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / Ribosomal protein S26e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / 40S Ribosomal protein S10 / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / S27a-like superfamily / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L30e signature 1. / Ribosomal L40e family / Ribosomal protein L36e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / : / Ribosomal protein S25 / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / S25 ribosomal protein / : / Ribosomal_L40e / Ribosomal protein L27e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L44e / Ribosomal Protein L6, KOW domain / Ribosomal protein L44 / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein 60S L18 and 50S L18e / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S7e signature. / 60S ribosomal protein L35 / Ribosomal protein S27a / Ribosomal protein S27a
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60s ribosomal protein l27a-3 / 60S ribosomal protein L35-like / 60S ribosomal protein L30 / 60S ribosomal protein L11-1 / 60S ribosomal protein L27 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60s ribosomal protein l27a-3 / 60S ribosomal protein L35-like / 60S ribosomal protein L30 / 60S ribosomal protein L11-1 / 60S ribosomal protein L27 / 60S ribosomal protein L21-1-like / 60S ribosomal protein L5-like / 40S ribosomal protein S30 / 40S ribosomal protein S20-2 / Ribosomal protein L15 / 60S ribosomal protein L23 / 60S ribosomal protein L8-like / Ribosomal protein / 60S ribosomal protein L31 / 60S ribosomal protein L10 / 40S ribosomal protein S6 / Large ribosomal subunit protein uL13w / 40S ribosomal protein S7 / Small ribosomal subunit protein eS17-like / 60S ribosomal protein L3 / 40S ribosomal protein S13 / 40S ribosomal protein S24 / 40S ribosomal protein S26 / Ribosomal protein L19 / Large ribosomal subunit protein eL33y-like / Small ribosomal subunit protein uS13z/uS13y/uS13x / 40S ribosomal protein S16 / 40S ribosomal protein S5 / 40S ribosomal protein S12 / 40S ribosomal protein S27 / 60S ribosomal protein L24 / Large ribosomal subunit protein eL22 / 40S ribosomal protein S11 / Large ribosomal subunit protein uL4-like / 40S ribosomal protein S21 / 60S ribosomal protein L38 / Large ribosomal subunit protein uL24z / Large ribosomal subunit protein uL6z/uL6y / 60S ribosomal protein L13 / Small ribosomal subunit protein eS19x-like / 40S ribosomal protein S8 / 60S ribosomal protein L18-2 / 40S ribosomal protein S10-1 / Ribosomal protein L37 / 40S ribosomal protein S4 / Large ribosomal subunit protein uL22z / Large ribosomal subunit protein eL14z / 40S ribosomal protein S25 / Small ribosomal subunit protein uS14z/uS14y/uS14x / 60S ribosomal protein L18a / 40S ribosomal protein S28 / 60S ribosomal protein L36 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS2 / Ubiquitin-ribosomal protein eS31 fusion protein-like / Large ribosomal subunit protein eL6-like / Small ribosomal subunit protein uS3y-like / Large ribosomal subunit protein eL28z-like / Small ribosomal subunit protein uS19-like / Large ribosomal subunit protein uL30w-like / Small ribosomal subunit protein uS4y-like / Small ribosomal subunit protein uS11y / Ubiquitin-ribosomal protein eL40 fusion protein / 60S ribosomal protein L7a / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL39x / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL32z / Small ribosomal subunit protein uS8c / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS1
Similarity search - Component
Biological speciesNicotiana benthamiana (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsLu, G. / Lin, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130063 China
National Natural Science Foundation of China (NSFC)32471349 China
CitationJournal: To be published
Title: cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S
Authors: Lu, G. / Lin, J.
History
DepositionJul 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
SA: Small ribosomal subunit protein uS2
SB: 30S ribosomal protein S3, chloroplastic
SC: 40S ribosomal protein S9-2-like
SD: Small ribosomal subunit protein uS5
SE: 40S ribosomal protein S5
SF: Small ribosomal subunit protein uS8c
SG: 40S ribosomal protein S16
SH: 40S ribosomal protein S20-2
SI: 40S ribosomal protein S14-2
SJ: 40S ribosomal protein S23
SK: 40S ribosomal protein S18
SL: 40S ribosomal protein S29
SM: 40S ribosomal protein S13
SN: 40S ribosomal protein S11
SO: 40S ribosomal protein S15-like
SP: Small ribosomal subunit protein eS1
SQ: 40S ribosomal protein S4
SR: 40S ribosomal protein S6
SS: 40S ribosomal protein S7
ST: 40S ribosomal protein S8
SU: 40S ribosomal protein S10-1
SV: 40S ribosomal protein S12
SW: 40S ribosomal protein S17-like
SX: 40S ribosomal protein S19-3-like
SY: 40S ribosomal protein S21
SZ: 40S ribosomal protein S24
Sa: 40S ribosomal protein S25
Sb: 40S ribosomal protein S26
Sc: 40S ribosomal protein S27
Sd: 40S ribosomal protein S28
Se: 40S ribosomal protein S30
Sf: Ubiquitin-40S ribosomal protein S27a-like
LA: Ribosomal protein
LB: 60S ribosomal protein L8-like
LC: 60S ribosomal protein L3
LD: 60S ribosomal protein L4-like
LE: 60S ribosomal protein L11-1
LF: 60S ribosomal protein L9-1
LG: 60S ribosomal protein L13a-4
LH: 60S ribosomal protein L23
LI: 60s ribosomal protein l27a-3
LJ: 60S ribosomal protein L10
LK: 60S ribosomal protein L5-like
LL: 60S ribosomal protein L17-1 isoform X2
LM: Large ribosomal subunit protein uL23
LN: 60S ribosomal protein L26-1
LO: 60S ribosomal protein L35-like
LP: 60S ribosomal protein L7-4-like
LQ: 60S ribosomal protein L6-like isoform X1
LR: 60S ribosomal protein L7a
LS: 60S ribosomal protein L13
LT: 60S ribosomal protein L14-1
LU: Ribosomal protein L15
LV: 60S ribosomal protein L18-2
LW: Ribosomal protein L19
LX: 60S ribosomal protein L18a
LY: 60S ribosomal protein L21-1-like
LZ: Large ribosomal subunit protein eL22
La: 60S ribosomal protein L24
Lb: 60S ribosomal protein L27
Lc: 60S ribosomal protein L28-1-like
Ld: 60S ribosomal protein L29
Le: 60S ribosomal protein L30
Lf: 60S ribosomal protein L31
Lg: 60S ribosomal protein L32-1
Lh: 60S ribosomal protein L35a-3-like
Li: Large ribosomal subunit protein eL34
Lj: 60S ribosomal protein L36
Lk: Ribosomal protein L37
Ll: 60S ribosomal protein L38
Lm: 60S ribosomal protein L39-3
Ln: Ubiquitin-60S ribosomal protein L40
Lo: 60s ribosomal protein l41-like
Lp: 60S ribosomal protein L44
Lq: 60S ribosomal protein L37a
10: 25S rRNA
11: 18S rRNA
12: 5S rRNA
13: 5.8S rRNA
14: 25S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,214,15389
Polymers3,213,93480
Non-polymers2199
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Small ribosomal subunit protein ... , 4 types, 4 molecules SASDSFSP

#1: Protein Small ribosomal subunit protein uS2


Mass: 28579.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence reference for strain 'Nicotiana benthamiana' is not available in UniProt at the time of biocuration.
Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7W513
#4: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2


Mass: 30697.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7Y544
#6: Protein Small ribosomal subunit protein uS8c


Mass: 14815.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7YEG5
#16: Protein Small ribosomal subunit protein eS1 / 40S ribosomal protein S3a / Protein cyc07


Mass: 29782.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: Q285L8

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Protein , 4 types, 4 molecules SBSfLALn

#2: Protein 30S ribosomal protein S3, chloroplastic


Mass: 27746.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7WQT4
#32: Protein Ubiquitin-40S ribosomal protein S27a-like


Mass: 17739.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7WCX2
#33: Protein Ribosomal protein


Mass: 24778.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3Y379
#72: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14703.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7X7W2

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40S ribosomal protein ... , 26 types, 26 molecules SCSESGSHSISJSKSLSMSNSOSQSRSSSTSUSVSWSXSYSZSaSbScSdSe

#3: Protein 40S ribosomal protein S9-2-like


Mass: 22070.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7X6K6
#5: Protein 40S ribosomal protein S5


Mass: 23374.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4AYA1
#7: Protein 40S ribosomal protein S16


Mass: 16731.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4AU23
#8: Protein 40S ribosomal protein S20-2


Mass: 13651.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XHL0
#9: Protein 40S ribosomal protein S14-2


Mass: 16375.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7X6S8
#10: Protein 40S ribosomal protein S23


Mass: 15771.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7W217
#11: Protein 40S ribosomal protein S18


Mass: 16374.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4AJE0
#12: Protein 40S ribosomal protein S29


Mass: 6455.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7V0A7
#13: Protein 40S ribosomal protein S13


Mass: 17099.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3ZRI7
#14: Protein 40S ribosomal protein S11


Mass: 17724.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4BW10
#15: Protein 40S ribosomal protein S15-like


Mass: 17274.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7X1Z5
#17: Protein 40S ribosomal protein S4


Mass: 29971.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4DQ51
#18: Protein 40S ribosomal protein S6


Mass: 28355.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3Z3Y7
#19: Protein 40S ribosomal protein S7


Mass: 22164.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3Z906
#20: Protein 40S ribosomal protein S8


Mass: 24166.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4CZK3
#21: Protein 40S ribosomal protein S10-1


Mass: 13924.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4DHU6
#22: Protein 40S ribosomal protein S12


Mass: 15147.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4BEE0
#23: Protein 40S ribosomal protein S17-like


Mass: 15091.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3Z9G2
#24: Protein 40S ribosomal protein S19-3-like


Mass: 16034.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4CYT7
#25: Protein 40S ribosomal protein S21


Mass: 9304.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4C2G0
#26: Protein 40S ribosomal protein S24


Mass: 15429.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3ZXI6
#27: Protein 40S ribosomal protein S25


Mass: 8325.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7UZX1
#28: Protein 40S ribosomal protein S26


Mass: 13206.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4A5C8
#29: Protein 40S ribosomal protein S27


Mass: 9497.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4BH20
#30: Protein 40S ribosomal protein S28


Mass: 7481.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7VNF8
#31: Protein 40S ribosomal protein S30


Mass: 6953.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XGJ0

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60S ribosomal protein ... , 35 types, 35 molecules LBLCLDLELFLGLHLILJLKLLLNLOLPLQLRLSLTLVLXLYLaLbLcLdLeLfLgLhLj...

#34: Protein 60S ribosomal protein L8-like


Mass: 28220.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XXQ5
#35: Protein 60S ribosomal protein L3


Mass: 44552.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3ZLI9
#36: Protein 60S ribosomal protein L4-like


Mass: 44778.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4BWA4
#37: Protein 60S ribosomal protein L11-1


Mass: 20794.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XAW1
#38: Protein 60S ribosomal protein L9-1


Mass: 22058.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4CJ62
#39: Protein 60S ribosomal protein L13a-4


Mass: 23583.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3Z662
#40: Protein 60S ribosomal protein L23 / Large ribosomal subunit protein uL14


Mass: 15040.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XSQ1
#41: Protein 60s ribosomal protein l27a-3


Mass: 16504.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1J6IJF4
#42: Protein 60S ribosomal protein L10


Mass: 24841.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3Z2D7
#43: Protein 60S ribosomal protein L5-like


Mass: 33691.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XE16
#44: Protein 60S ribosomal protein L17-1 isoform X2


Mass: 19906.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4DQP0
#46: Protein 60S ribosomal protein L26-1


Mass: 16808.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4CC07
#47: Protein 60S ribosomal protein L35-like


Mass: 14324.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3WY31
#48: Protein 60S ribosomal protein L7-4-like


Mass: 28147.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7X2X8
#49: Protein 60S ribosomal protein L6-like isoform X1


Mass: 25493.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7WD54
#50: Protein 60S ribosomal protein L7a


Mass: 27223.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7XNI3
#51: Protein 60S ribosomal protein L13


Mass: 22862.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4CSN1
#52: Protein 60S ribosomal protein L14-1


Mass: 15027.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7UYX7
#54: Protein 60S ribosomal protein L18-2


Mass: 20905.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4DF55
#56: Protein 60S ribosomal protein L18a


Mass: 21513.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7V5H1
#57: Protein 60S ribosomal protein L21-1-like


Mass: 18716.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XCW6
#59: Protein 60S ribosomal protein L24


Mass: 18606.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4BHF2
#60: Protein 60S ribosomal protein L27


Mass: 15692.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XBV7
#61: Protein 60S ribosomal protein L28-1-like


Mass: 15987.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7WYY1
#62: Protein/peptide 60S ribosomal protein L29


Mass: 5914.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant)
#63: Protein 60S ribosomal protein L30


Mass: 12420.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3WZ09
#64: Protein 60S ribosomal protein L31


Mass: 13894.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3Y3V5
#65: Protein 60S ribosomal protein L32-1


Mass: 15637.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7YAK1
#66: Protein 60S ribosomal protein L35a-3-like


Mass: 12959.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4AHL7
#68: Protein 60S ribosomal protein L36


Mass: 12389.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7VXX3
#70: Protein 60S ribosomal protein L38


Mass: 8101.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4C4G8
#71: Protein 60S ribosomal protein L39-3


Mass: 6503.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7Y1K3
#73: Protein/peptide 60s ribosomal protein l41-like


Mass: 3443.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant)
#74: Protein 60S ribosomal protein L44


Mass: 11991.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7YPT7
#75: Protein 60S ribosomal protein L37a


Mass: 8624.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1U7XSD1

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Large ribosomal subunit protein ... , 3 types, 3 molecules LMLZLi

#45: Protein Large ribosomal subunit protein uL23 / 60S ribosomal protein L23a / L25


Mass: 17355.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: Q07761
#58: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 12506.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4BSU3
#67: Protein Large ribosomal subunit protein eL34 / 60S ribosomal protein L34


Mass: 13788.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: P41098

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Ribosomal protein ... , 3 types, 3 molecules LULWLk

#53: Protein Ribosomal protein L15


Mass: 24226.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S3XIA7
#55: Protein Ribosomal protein L19


Mass: 24742.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4A7M5
#69: Protein Ribosomal protein L37


Mass: 10879.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: UniProt: A0A1S4DN51

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RNA chain , 5 types, 5 molecules 1011121314

#76: RNA chain 25S rRNA


Mass: 65633.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant)
#77: RNA chain 18S rRNA


Mass: 582853.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant) / References: GenBank: 806909817
#78: RNA chain 5S rRNA


Mass: 38328.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant)
#79: RNA chain 5.8S rRNA


Mass: 52534.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant)
#80: RNA chain 25S rRNA


Mass: 1097118.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana benthamiana (plant)

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Non-polymers , 2 types, 43 molecules

#81: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#82: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: tobacco 80S ribosome with tRNA-like structure / Type: RIBOSOME / Entity ID: #1-#75, #77-#79, #76 / Source: NATURAL
Source (natural)Organism: Nicotiana benthamiana (plant)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)

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Processing

EM software
IDNameCategory
1EPUparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 422599 / Symmetry type: POINT

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