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- PDB-9hes: Structure of the Arabidopsis thaliana 80S ribosome OVAC mutant in... -

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Basic information

Entry
Database: PDB / ID: 9hes
TitleStructure of the Arabidopsis thaliana 80S ribosome OVAC mutant in complex with P- and E-site tRNAs, mRNA, and thermospermine
Components
  • (Large ribosomal subunit protein ...) x 37
  • (Ribosomal RNA ...) x 4
  • (Ribosomal protein ...) x 2
  • (Small ribosomal subunit protein ...) x 31
  • 60S ribosomal protein L29
  • Messenger RNA
  • Nascent polypeptide
  • Transfer RNA Phe GAA
  • Ubiquitin-ribosomal protein eL40z fusion protein
KeywordsRIBOSOME / thermospermine / thaliana / polyamines / ovac / 3-methyluridine
Function / homology
Function and homology information


root morphogenesis / trichome morphogenesis / cytokinesis by cell plate formation / adaxial/abaxial pattern specification / leaf morphogenesis / response to high light intensity / plant-type cell wall / developmental process / chloroplast envelope / plasmodesma ...root morphogenesis / trichome morphogenesis / cytokinesis by cell plate formation / adaxial/abaxial pattern specification / leaf morphogenesis / response to high light intensity / plant-type cell wall / developmental process / chloroplast envelope / plasmodesma / plant-type vacuole / vacuole / response to UV-B / response to osmotic stress / nucleocytoplasmic transport / plastid / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / maturation of LSU-rRNA / response to salt stress / 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) / cytosolic ribosome / response to cold / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation / small-subunit processome / modification-dependent protein catabolic process / protein tag activity / rRNA processing / peroxisome / ribosome biogenesis / ribosomal small subunit assembly / ribosomal small subunit biogenesis / response to oxidative stress / 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 / defense response to bacterium / rRNA binding / structural constituent of ribosome / protein ubiquitination / ribosome / translation / ribonucleoprotein complex / cell division / mRNA binding / ubiquitin protein ligase binding / nucleolus / endoplasmic reticulum / mitochondrion / RNA binding / extracellular region / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / : / : / : / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type ...: / : / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L28e / : / : / : / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S21e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L44e signature. / Ribosomal protein L10e signature. / Ribosomal protein L19/L19e conserved site / 40S Ribosomal protein S10 / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L10e / Plectin/S10, N-terminal / Plectin/S10 domain / 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 S30 / : / Ribosomal protein S30 / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal L40e family / Ribosomal protein S7e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L30e signature 1. / Ribosomal protein L36e signature. / Ribosomal protein S8e subdomain, eukaryotes / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L35Ae, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L35Ae signature. / Ribosomal protein S17e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S17e signature. / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal Protein L6, KOW domain / Ribosomal protein S3Ae, conserved site / 60S ribosomal protein L35 / Ribosomal protein S3Ae signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature.
Similarity search - Domain/homology
: / SPERMIDINE / Chem-TER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...: / SPERMIDINE / Chem-TER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L18ae/LX family protein / Ubiquitin-ribosomal protein eL40z fusion protein / Ribosomal protein L30/L7 family protein / 60S ribosomal protein L29 / Large ribosomal subunit protein eL38z/eL38y / Large ribosomal subunit protein eL42z/eL42y / Large ribosomal subunit protein eL15z / Large ribosomal subunit protein eL28z / Small ribosomal subunit protein uS17z / Large ribosomal subunit protein uL3z / Small ribosomal subunit protein uS13z/uS13y/uS13x / Small ribosomal subunit protein eS28x / Large ribosomal subunit protein eL13z / Large ribosomal subunit protein uL5z / Small ribosomal subunit protein uS8z/uS8w / Large ribosomal subunit protein uL2z / Small ribosomal subunit protein uS12y / Small ribosomal subunit protein eS26y / Large ribosomal subunit protein uL6z/uL6y / Large ribosomal subunit protein eL32z / Large ribosomal subunit protein uL15x / Small ribosomal subunit protein eS30z/eS30y/eS30x / Large ribosomal subunit protein uL14x/uL14z/uL14y / Large ribosomal subunit protein uL24z / Large ribosomal subunit protein eL27x / Large ribosomal subunit protein eL39z/eL39x / Small ribosomal subunit protein uS7y / Small ribosomal subunit protein eS6y / Small ribosomal subunit protein uS15y / Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v / Small ribosomal subunit protein uS2z / Large ribosomal subunit protein uL16y / Small ribosomal subunit protein eS21y / Small ribosomal subunit protein eS1y / Large ribosomal subunit protein eL24z / Large ribosomal subunit protein eL34z / Large ribosomal subunit protein eL21z/eL21y / Small ribosomal subunit protein uS14z/uS14y/uS14x / Large ribosomal subunit protein uL18z / Small ribosomal subunit protein eS24y / Small ribosomal subunit protein eS7x / Large ribosomal subunit protein eL37z / Large ribosomal subunit protein eL43y / Small ribosomal subunit protein eS4x / Large ribosomal subunit protein eL30y / Small ribosomal subunit protein uS5y/uS5u/uS5v / Small ribosomal subunit protein eS8z / Large ribosomal subunit protein uL22z / Large ribosomal subunit protein eL18x / Large ribosomal subunit protein eL33y / Large ribosomal subunit protein eL6y / Small ribosomal subunit protein uS11y / Small ribosomal subunit protein uS4y / Small ribosomal subunit protein eS19x / Small ribosomal subunit protein uS19y / Large ribosomal subunit protein uL13y / Small ribosomal subunit protein eS17w / Large ribosomal subunit protein eL8y / Small ribosomal subunit protein eS27y / Large ribosomal subunit protein eL36y / Large ribosomal subunit protein uL23y / Large ribosomal subunit protein uL29x / Large ribosomal subunit protein eL22z / Large ribosomal subunit protein uL4z / Small ribosomal subunit protein uS3z / Small ribosomal subunit protein uS9z / Large ribosomal subunit protein eL19x / Large ribosomal subunit protein eL31y / Small ribosomal subunit protein uS10y / Small ribosomal subunit protein eS10z / Small ribosomal subunit protein eS25w / Large ribosomal subunit protein eL14y
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsFaille, A. / Warren, A.J.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
Gatsby Charitable FoundationGAT3395/PR3 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N013158/1 United Kingdom
European Research Council (ERC)323052European Union
CitationJournal: Science / Year: 2026
Title: Structure of the Arabidopsis thaliana 80S ribosome in complex with P- and E-site tRNAs and mRNA
Authors: Faille, A. / Warren, A.J. / Hellmann, E. / Ko, D. / Ruonala, R. / Helariutta, Y.E.
History
DepositionNov 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
3: Ribosomal RNA 5.8S
A: Ribosomal RNA 25S
2: Transfer RNA Phe GAA
C3: Ribosomal RNA 5S
BC: Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v
BM: Large ribosomal subunit protein uL22z
BO: Large ribosomal subunit protein uL24z
AR: 60S ribosomal protein L29
AU: Large ribosomal subunit protein eL31y
Ma: Small ribosomal subunit protein eS26y
Ia: Large ribosomal subunit protein uL6z/uL6y
AE: Small ribosomal subunit protein uS8z/uS8w
AX: Large ribosomal subunit protein eL36y
AP: Large ribosomal subunit protein eL27x
Ja: Small ribosomal subunit protein eS4x
Ea: Large ribosomal subunit protein eL15z
AL: Ribosomal protein L18ae/LX family protein
Va: Small ribosomal subunit protein uS12y
Ka: Small ribosomal subunit protein eS24y
AW: Large ribosomal subunit protein eL33y
BD: Large ribosomal subunit protein eL42z/eL42y
BS: Large ribosomal subunit protein uL3z
AM: Large ribosomal subunit protein eL21z/eL21y
AC: Small ribosomal subunit protein uS5y/uS5u/uS5v
BI: Large ribosomal subunit protein uL14x/uL14z/uL14y
AH: Large ribosomal subunit protein eL14y
BT: Large ribosomal subunit protein uL4z
AV: Large ribosomal subunit protein eL32z
AD: Small ribosomal subunit protein uS7y
AJ: Large ribosomal subunit protein eL18x
BQ: Large ribosomal subunit protein uL2z
BH: Large ribosomal subunit protein uL13y
Da: Small ribosomal subunit protein uS15y
BK: Large ribosomal subunit protein uL18z
AT: Large ribosomal subunit protein eL30y
Pa: Small ribosomal subunit protein eS30z/eS30y/eS30x
BP: Large ribosomal subunit protein uL29x
BN: Large ribosomal subunit protein uL23y
BG: Large ribosomal subunit protein eL8y
Fa: Large ribosomal subunit protein eL34z
Ha: Large ribosomal subunit protein uL15x
BU: Large ribosomal subunit protein uL5z
BR: Ribosomal protein L30/L7 family protein
Xa: Small ribosomal subunit protein uS17z
BV: Small ribosomal subunit protein eS1y
BJ: Large ribosomal subunit protein uL16y
AO: Large ribosomal subunit protein eL24z
BW: Small ribosomal subunit protein eS21y
AK: Large ribosomal subunit protein eL19x
Na: Small ribosomal subunit protein eS27y
AB: Small ribosomal subunit protein uS4y
BF: Large ribosomal subunit protein eL6y
AA: Small ribosomal subunit protein uS3z
AG: Large ribosomal subunit protein eL13z
Ga: Ubiquitin-ribosomal protein eL40z fusion protein
BA: Large ribosomal subunit protein eL39z/eL39x
AF: Small ribosomal subunit protein uS9z
Wa: Small ribosomal subunit protein uS13z/uS13y/uS13x
Ta: Small ribosomal subunit protein eS6y
AZ: Large ribosomal subunit protein eL38z/eL38y
BE: Large ribosomal subunit protein eL43y
Za: Small ribosomal subunit protein uS2z
AQ: Large ribosomal subunit protein eL28z
Oa: Small ribosomal subunit protein eS28x
Ua: Small ribosomal subunit protein uS11y
Ya: Small ribosomal subunit protein uS19y
BB: Small ribosomal subunit protein eS17w
AN: Large ribosomal subunit protein eL22z
Ra: Small ribosomal subunit protein eS7x
BL: Small ribosomal subunit protein eS19x
La: Small ribosomal subunit protein eS25w
Aa: Small ribosomal subunit protein eS8z
AY: Large ribosomal subunit protein eL37z
Ca: Small ribosomal subunit protein uS14z/uS14y/uS14x
h1: Ribosomal RNA 18S
B1: Messenger RNA
W2: Transfer RNA Phe GAA
Ba: Small ribosomal subunit protein uS10y
AI: Small ribosomal subunit protein eS10z
L3: Nascent polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,199,908590
Polymers3,179,37280
Non-polymers20,536510
Water191,96810656
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
112
21W2

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: A / End label comp-ID: A / Auth seq-ID: 1 - 76 / Label seq-ID: 1 - 76

Dom-IDAuth asym-IDLabel asym-ID
12C
2W2YB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Ribosomal RNA ... , 4 types, 4 molecules 3AC3h1

#1: RNA chain Ribosomal RNA 5.8S


Mass: 52827.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: GenBank: 731187285
#2: RNA chain Ribosomal RNA 25S


Mass: 1096380.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#4: RNA chain Ribosomal RNA 5S


Mass: 38917.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: GenBank: 2442578393
#75: RNA chain Ribosomal RNA 18S


Mass: 582777.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)

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RNA chain , 2 types, 3 molecules 2W2B1

#3: RNA chain Transfer RNA Phe GAA


Mass: 24571.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: GenBank: 19120
#76: RNA chain Messenger RNA


Mass: 3629.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)

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Small ribosomal subunit protein ... , 31 types, 31 molecules BCMaAEJaVaKaACADDaPaXaBVBWNaABAAAFWaTaZaOaUaYaBBRaBLLaAaCaBaAI

#5: Protein/peptide Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v / 60S ribosomal protein L41 / Large ribosomal subunit protein eL41z/eL41y/eL41x/eL41w/eL41v


Mass: 3445.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62120
#10: Protein Small ribosomal subunit protein eS26y / 40S ribosomal protein S26-1


Mass: 14762.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49206
#12: Protein Small ribosomal subunit protein uS8z/uS8w / 40S ribosomal protein S15a-1


Mass: 14829.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P42798
#15: Protein Small ribosomal subunit protein eS4x / 40S ribosomal protein S4-3


Mass: 29875.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8VYK6
#18: Protein Small ribosomal subunit protein uS12y / 40S ribosomal protein S23-2 / S12


Mass: 15770.618 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49201
#19: Protein Small ribosomal subunit protein eS24y / 40S ribosomal protein S24-2


Mass: 15458.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LC83
#24: Protein Small ribosomal subunit protein uS5y/uS5u/uS5v / 40S ribosomal protein S2-2


Mass: 30826.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q93VB8
#29: Protein Small ribosomal subunit protein uS7y / 40S ribosomal protein S5-2 / AtRPS5A / Protein ARABIDOPSIS MINUTE-LIKE 1


Mass: 22956.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P51427
#33: Protein Small ribosomal subunit protein uS15y / 40S ribosomal protein S13-2


Mass: 17123.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P59224
#36: Protein Small ribosomal subunit protein eS30z/eS30y/eS30x / 40S ribosomal protein S30


Mass: 6910.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49689
#44: Protein Small ribosomal subunit protein uS17z / 40S ribosomal protein S11-1 / Protein EMBRYO DEFECTIVE 1080


Mass: 17996.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P16181
#45: Protein Small ribosomal subunit protein eS1y / 40S ribosomal protein S3a-2


Mass: 29857.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q42262
#48: Protein Small ribosomal subunit protein eS21y / 40S ribosomal protein S21-2


Mass: 9125.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q3E902
#50: Protein Small ribosomal subunit protein eS27y / 40S ribosomal protein S27-2


Mass: 9614.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M2F1
#51: Protein Small ribosomal subunit protein uS4y / 40S ribosomal protein S9-2


Mass: 23207.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FLF0
#53: Protein Small ribosomal subunit protein uS3z / 40S ribosomal protein S3-1


Mass: 27559.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SIP7
#57: Protein Small ribosomal subunit protein uS9z / 40S ribosomal protein S16-1


Mass: 16663.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SK22
#58: Protein Small ribosomal subunit protein uS13z/uS13y/uS13x / 40S ribosomal protein S18


Mass: 17582.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P34788
#59: Protein Small ribosomal subunit protein eS6y / 40S ribosomal protein S6-2 / Protein EMBRYO DEFECTIVE 3010


Mass: 28228.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P51430
#62: Protein Small ribosomal subunit protein uS2z / 40S ribosomal protein Sa-1 / Laminin receptor homolog / p40


Mass: 32320.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q08682
#64: Protein Small ribosomal subunit protein eS28x / 40S ribosomal protein S28-2


Mass: 7355.558 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P34789
#65: Protein Small ribosomal subunit protein uS11y / 40S ribosomal protein S14-2


Mass: 16303.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9CAX6
#66: Protein Small ribosomal subunit protein uS19y / 40S ribosomal protein S15-3


Mass: 16781.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FY65
#67: Protein Small ribosomal subunit protein eS17w / 40S ribosomal protein S17-4


Mass: 16048.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LZ17
#69: Protein Small ribosomal subunit protein eS7x / 40S ribosomal protein S7-3


Mass: 22101.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LD03
#70: Protein Small ribosomal subunit protein eS19x / 40S ribosomal protein S19-3


Mass: 15726.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FNP8
#71: Protein Small ribosomal subunit protein eS25w / 40S ribosomal protein S25-4


Mass: 12079.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9T029
#72: Protein Small ribosomal subunit protein eS8z / 40S ribosomal protein S8-1


Mass: 25047.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q93VG5
#74: Protein Small ribosomal subunit protein uS14z/uS14y/uS14x / 40S ribosomal protein S29


Mass: 6443.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q680P8
#77: Protein Small ribosomal subunit protein uS10y / 40S ribosomal protein S20-2


Mass: 13718.138 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9STY6
#78: Protein Small ribosomal subunit protein eS10z / 40S ribosomal protein S10-1


Mass: 19475.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SW09

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Large ribosomal subunit protein ... , 37 types, 37 molecules BMBOAUIaAXAPEaAWBDBSAMBIAHBTAVAJBQBHBKATBPBNBGFaHaBUBJAOAKBF...

#6: Protein Large ribosomal subunit protein uL22z / 60S ribosomal protein L17-1


Mass: 19937.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q93VI3
#7: Protein Large ribosomal subunit protein uL24z / 60S ribosomal protein L26-1


Mass: 16983.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P51414
#9: Protein Large ribosomal subunit protein eL31y / 60S ribosomal protein L31-2


Mass: 13852.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9STR1
#11: Protein Large ribosomal subunit protein uL6z/uL6y / 60S ribosomal protein L9-1


Mass: 22059.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49209
#13: Protein Large ribosomal subunit protein eL36y / 60S ribosomal protein L36-2


Mass: 12713.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M352
#14: Protein Large ribosomal subunit protein eL27x / 60S ribosomal protein L27-3


Mass: 15644.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P51419
#16: Protein Large ribosomal subunit protein eL15z / 60S ribosomal protein L15-1


Mass: 24297.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O23515
#20: Protein Large ribosomal subunit protein eL33y / 60S ribosomal protein L35a-3


Mass: 12941.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C912
#21: Protein Large ribosomal subunit protein eL42z/eL42y / 60S ribosomal protein L36a


Mass: 12160.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O23290
#22: Protein Large ribosomal subunit protein uL3z / 60S ribosomal protein L3-1 / Protein EMBRYO DEFECTIVE 2207


Mass: 44666.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P17094
#23: Protein Large ribosomal subunit protein eL21z/eL21y / 60S ribosomal protein L21-1


Mass: 18693.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q43291
#25: Protein Large ribosomal subunit protein uL14x/uL14z/uL14y / 60S ribosomal protein L23 / Protein EMBRYO DEFECTIVE 2171


Mass: 15052.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49690
#26: Protein Large ribosomal subunit protein eL14y / 60S ribosomal protein L14-2


Mass: 15536.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9T043
#27: Protein Large ribosomal subunit protein uL4z / 60S ribosomal protein L4-1 / L1


Mass: 44783.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SF40
#28: Protein Large ribosomal subunit protein eL32z / 60S ribosomal protein L32-1


Mass: 15539.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49211
#30: Protein Large ribosomal subunit protein eL18x / 60S ribosomal protein L18-3


Mass: 21012.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q940B0
#31: Protein Large ribosomal subunit protein uL2z / 60S ribosomal protein L2 / 60S ribosomal protein L8-1 / Protein EMBRYO DEFECTIVE 2296


Mass: 27918.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P46286
#32: Protein Large ribosomal subunit protein uL13y / 60S ribosomal protein L13a-2


Mass: 23510.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LRX8
#34: Protein Large ribosomal subunit protein uL18z / 60S ribosomal protein L5-1 / Ribosomal protein L5 A / Protein ASYMMETRIC LEAVES1/2 ENHANCER 6 / ...60S ribosomal protein L5-1 / Ribosomal protein L5 A / Protein ASYMMETRIC LEAVES1/2 ENHANCER 6 / Protein OLIGOCELLULA 5 / Protein PIGGYBACK 3


Mass: 34420.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LBI1
#35: Protein Large ribosomal subunit protein eL30y / 60S ribosomal protein L30-2


Mass: 12311.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8VZ19
#37: Protein Large ribosomal subunit protein uL29x / 60S ribosomal protein L35-3


Mass: 14215.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M3D2
#38: Protein Large ribosomal subunit protein uL23y / 60S ribosomal protein L23a-2


Mass: 17436.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M3C3
#39: Protein Large ribosomal subunit protein eL8y / 60S ribosomal protein L7a-2


Mass: 29095.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LZH9
#40: Protein Large ribosomal subunit protein eL34z / 60S ribosomal protein L34-1


Mass: 13740.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q42351
#41: Protein Large ribosomal subunit protein uL15x / 60S ribosomal protein L27a-3


Mass: 16498.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49637
#42: Protein Large ribosomal subunit protein uL5z / 60S ribosomal protein L11-1 / L16A


Mass: 20867.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P42795
#46: Protein Large ribosomal subunit protein uL16y / 60S ribosomal protein L10-2 / Wilms tumor suppressor protein homolog


Mass: 24962.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q08770
#47: Protein Large ribosomal subunit protein eL24z / 60S ribosomal protein L24-1


Mass: 18900.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q42347
#49: Protein Large ribosomal subunit protein eL19x / 60S ribosomal protein L19-1 / Protein EMBRYO DEFECTIVE 2386


Mass: 24676.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SRX2
#52: Protein Large ribosomal subunit protein eL6y / 60S ribosomal protein L6-2


Mass: 26062.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C9C6
#54: Protein Large ribosomal subunit protein eL13z / 60S ribosomal protein L13-1 / Protein BBC1 homolog


Mass: 23824.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P41127
#56: Protein Large ribosomal subunit protein eL39z/eL39x / 60S ribosomal protein L39-1


Mass: 6435.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P51424
#60: Protein Large ribosomal subunit protein eL38z/eL38y / 60S ribosomal protein L38


Mass: 8139.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O22860
#61: Protein Large ribosomal subunit protein eL43y / 60S ribosomal protein L37a-2


Mass: 10264.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8RXU5
#63: Protein Large ribosomal subunit protein eL28z / 60S ribosomal protein L28-1 / Protein ASYMMETRIC LEAVES1/2 ENHANCER 5


Mass: 15926.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O82204
#68: Protein Large ribosomal subunit protein eL22z / 60S ribosomal protein L22-2


Mass: 14045.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M9W1
#73: Protein Large ribosomal subunit protein eL37z / 60S ribosomal protein L37-1


Mass: 10844.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LFH7

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Protein , 2 types, 2 molecules ARGa

#8: Protein 60S ribosomal protein L29


Mass: 9410.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4JC32
#55: Protein Ubiquitin-ribosomal protein eL40z fusion protein


Mass: 14790.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: B9DHA6

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Ribosomal protein ... , 2 types, 2 molecules ALBR

#17: Protein Ribosomal protein L18ae/LX family protein


Mass: 25781.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A1P8AY36
#43: Protein Ribosomal protein L30/L7 family protein


Mass: 28573.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: F4IT48

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Protein/peptide , 1 types, 1 molecules L3

#79: Protein/peptide Nascent polypeptide


Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)

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Non-polymers , 7 types, 11166 molecules

#80: Chemical...
ChemComp-TER / N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE / THERMOSPERMINE / PA(334)


Mass: 202.340 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C10H26N4 / Feature type: SUBJECT OF INVESTIGATION
#81: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 289 / Source method: obtained synthetically / Formula: Mg
#82: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 186 / Source method: obtained synthetically / Formula: K
#83: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#84: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#85: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#86: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10656 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

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Experiment

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

-
Sample preparation

ComponentName: Ribosome in complex with P- and E-site tRNAs, mRNA, nascent peptide, and thermospermine molecules
Type: RIBOSOME / Entity ID: #1-#72, #79, #75-#78 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 53.85 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31655 / Symmetry type: POINT
RefinementResolution: 2.25→2.25 Å / Cor.coef. Fo:Fc: 0.762 / WRfactor Rwork: 0.379 / SU B: 7.969 / SU ML: 0.163 / Average fsc free: 0 / Average fsc overall: 0.7292 / Average fsc work: 0.7292 / ESU R: 0.202
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.379 4387527 -
all0.379 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 72.41 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.011211487
ELECTRON MICROSCOPYr_bond_other_d00.017139703
ELECTRON MICROSCOPYr_angle_refined_deg1.3021.851310357
ELECTRON MICROSCOPYr_angle_other_deg0.4441.757327651
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.653510502
ELECTRON MICROSCOPYr_dihedral_angle_2_deg5.05951009
ELECTRON MICROSCOPYr_dihedral_angle_other_2_deg0.66654034
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.761017144
ELECTRON MICROSCOPYr_dihedral_angle_6_deg14.527103736
ELECTRON MICROSCOPYr_chiral_restr0.0570.238616
ELECTRON MICROSCOPYr_chiral_restr_other0.0560.255
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.02163667
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0240480
ELECTRON MICROSCOPYr_nbd_refined0.190.236970
ELECTRON MICROSCOPYr_symmetry_nbd_other0.2160.2140680
ELECTRON MICROSCOPYr_nbtor_refined0.2190.287267
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0840.287275
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.2180.211988
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.1490.2138
ELECTRON MICROSCOPYr_metal_ion_refined0.1610.2577
ELECTRON MICROSCOPYr_mcbond_it7.5337.42242254
ELECTRON MICROSCOPYr_mcbond_other7.5337.42242254
ELECTRON MICROSCOPYr_mcangle_it11.70813.33552674
ELECTRON MICROSCOPYr_mcangle_other11.70813.33552675
ELECTRON MICROSCOPYr_scbond_it7.9527.864169233
ELECTRON MICROSCOPYr_scbond_other7.9527.864169234
ELECTRON MICROSCOPYr_scangle_it12.81614.208257683
ELECTRON MICROSCOPYr_scangle_other12.81614.208257684
ELECTRON MICROSCOPYr_lrange_it21.35889.779960877
ELECTRON MICROSCOPYr_lrange_other21.35889.779960878
ELECTRON MICROSCOPYr_ncsr_local_group_10.1830.057736
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
112ELECTRON MICROSCOPYLocal ncs0.183020.05007
12W2ELECTRON MICROSCOPYLocal ncs0.183020.05007
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.2-2.2571.8463246311.8463246310.1931.846
2.257-2.3190.7033165680.7033165680.4820.703
2.319-2.3860.6323077510.6323077510.5230.632
2.386-2.460.5652989610.5652989610.5720.565
2.46-2.540.5122896680.5122896680.6170.512
2.54-2.6290.4582801450.4582801450.6630.458
2.629-2.7290.4082703720.4082703720.7190.408
2.729-2.840.3692599830.3692599830.7740.369
2.84-2.9660.3442495670.3442495670.8390.344
2.966-3.1110.3362384030.3362384030.8990.336
3.111-3.2790.332268320.332268320.9360.33
3.279-3.4780.3092144120.3092144120.9490.309
3.478-3.7190.2772015810.2772015810.9540.277
3.719-4.0160.2461874940.2461874940.9580.246
4.016-4.40.2121725520.2121725520.9580.212
4.4-4.9190.1911560560.1911560560.9540.191
4.919-5.680.2231375330.2231375330.9450.223
5.68-6.9550.3491161450.3491161450.9270.349
6.955-9.8340.512897660.512897660.9260.512
9.834-309.0960.858491270.858491270.9320.858

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