[English] 日本語
Yorodumi
- PDB-9scu: Cryo-EM structure of the Arabidopsis thaliana 60S ribosomal subunit -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9scu
TitleCryo-EM structure of the Arabidopsis thaliana 60S ribosomal subunit
Components
  • (Large ribosomal subunit protein ...) x 36
  • (thale cress) hypothetical protein
  • 25S RNA
  • 60S ribosomal protein L29
  • RNA (119-MER)
  • RNA (151-MER)
  • Ribosomal protein L18ae/LX family protein
  • Ubiquitin-ribosomal protein eL40z fusion protein
KeywordsRIBOSOME / Arabidopsis / CryoEM
Function / homology
Function and homology information


root morphogenesis / response to fungus / adaxial/abaxial pattern specification / leaf morphogenesis / response to high light intensity / plant-type cell wall / developmental process / response to UV-B / plasmodesma / plant-type vacuole ...root morphogenesis / response to fungus / adaxial/abaxial pattern specification / leaf morphogenesis / response to high light intensity / plant-type cell wall / developmental process / response to UV-B / plasmodesma / plant-type vacuole / chloroplast envelope / vacuole / nucleocytoplasmic transport / plastid / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / response to cold / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / modification-dependent protein catabolic process / protein tag activity / cytosolic ribosome / large ribosomal subunit / cell division / response to oxidative stress / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / protein ubiquitination / ribonucleoprotein complex / structural constituent of ribosome / ribosome / translation / mRNA binding / nucleolus / endoplasmic reticulum / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / : / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. ...Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / : / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein 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 L38e / Ribosomal protein L13e / Ribosomal L38e protein family / Ribosomal protein L38e superfamily / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal L40e family / Ribosomal protein L36e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / : / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L44e / Ribosomal protein L44 / : / Ribosomal protein L7A/L8 / 60S ribosomal protein L35 / Ribosomal protein L6e / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 60S ribosomal protein L6E / Ribosomal protein L7, eukaryotic / : / Ribosomal protein L30, N-terminal / Ribosomal protein L39e, conserved site / Ribosomal L30 N-terminal domain / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L30/YlxQ / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / : / Ribosomal protein L18e / : / : / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L35A superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature.
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L18ae/LX family protein / (thale cress) hypothetical protein / Ubiquitin-ribosomal protein eL40z fusion protein ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L18ae/LX family protein / (thale cress) hypothetical protein / Ubiquitin-ribosomal protein eL40z fusion protein / 60S ribosomal protein L29 / Large ribosomal subunit protein eL38z/eL38y / Large ribosomal subunit protein eL42z/eL42y / Large ribosomal subunit protein uL3z / Large ribosomal subunit protein eL13z / Large ribosomal subunit protein eL18y / Large ribosomal subunit protein uL5z / Large ribosomal subunit protein uL6z/uL6y / Large ribosomal subunit protein eL32z / Large ribosomal subunit protein uL15x / Large ribosomal subunit protein uL14x/uL14z/uL14y / Large ribosomal subunit protein eL8z / Large ribosomal subunit protein uL24z / Large ribosomal subunit protein eL27x / Large ribosomal subunit protein eL31x / Large ribosomal subunit protein eL39z/eL39x / Large ribosomal subunit protein uL30y / Large ribosomal subunit protein uL16y / Large ribosomal subunit protein uL2x / Large ribosomal subunit protein eL24z / Large ribosomal subunit protein eL34z / Large ribosomal subunit protein uL18z / Large ribosomal subunit protein eL37z / Large ribosomal subunit protein eL15y / Large ribosomal subunit protein uL22z / Large ribosomal subunit protein eL6x / Large ribosomal subunit protein eL21x/eL21w / Large ribosomal subunit protein uL13w / Large ribosomal subunit protein eL33z / Large ribosomal subunit protein eL30x / Large ribosomal subunit protein eL19z / 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 / Large ribosomal subunit protein eL14z
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKarki, S. / Lu, X. / Paatero, A.O. / Ruonala, R. / Tranter, D. / Guryanov, S. / Rehan, S. / Hellmann, E. / Haakonsson, A. / Butcher, S.J. ...Karki, S. / Lu, X. / Paatero, A.O. / Ruonala, R. / Tranter, D. / Guryanov, S. / Rehan, S. / Hellmann, E. / Haakonsson, A. / Butcher, S.J. / Huiskonen, J.T. / Kajander, T. / Helariutta, Y. / Paavilainen, V.O.
Funding support United States, Finland, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132649[PVO1] United States
Academy of Finland338836 and 314672 Finland
CitationJournal: Structure / Year: 2026
Title: Cryo-EM structure of the Arabidopsis thaliana ribosome in translating and non-translating states.
Authors: Sudeep Karki / Xun Lu / Anja O Paatero / Raili Ruonala / Dale Tranter / Sergey Guryanov / Shahid Rehan / Eva Hellmann / Anders Haakonsson / Sarah J Butcher / Juha T Huiskonen / Tommi ...Authors: Sudeep Karki / Xun Lu / Anja O Paatero / Raili Ruonala / Dale Tranter / Sergey Guryanov / Shahid Rehan / Eva Hellmann / Anders Haakonsson / Sarah J Butcher / Juha T Huiskonen / Tommi Kajander / Yrjö Helariutta / Ville O Paavilainen /
Abstract: Translational control of mRNA expression underpins much of post-transcriptional gene expression driving developmental processes in eukaryotes. How ribosomal mRNA translation is executed in plants may ...Translational control of mRNA expression underpins much of post-transcriptional gene expression driving developmental processes in eukaryotes. How ribosomal mRNA translation is executed in plants may be especially important for adapting to an ever-changing environment. Arabidopsis thaliana is the main genetic model organism in plant science, yet structural insights into developmental processes where ribosomal gene expression plays important roles currently remain lacking. Here, we present cryoelectron microscopy (cryo-EM) structures of the Arabidopsis cytosolic ribosome in both translating and non-translating states, which together provide new structural details into how translation of cytosolic mRNAs is coordinated. Our structures reveal detailed information on the interactions of tRNAs, mRNA, and the nascent polypeptide with subunits of the actively translating 80S ribosome and the role of ribosomal RNA methylation in stabilizing ribosomal subunits. The structures provide a foundation for interpreting the functional effects of many mutations of ribosomal proteins affecting phenotypic effects for plant tissue development.
History
DepositionAug 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Aug 19, 2026Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.title / _em_admin.last_update
Revision 1.2Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.title / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
5: 25S RNA
Ck: Large ribosomal subunit protein eL38z/eL38y
CA: Large ribosomal subunit protein uL2x
CK: Large ribosomal subunit protein eL42z/eL42y
Cp: (thale cress) hypothetical protein
Cl: Large ribosomal subunit protein eL39z/eL39x
CY: Large ribosomal subunit protein uL24z
CL: Large ribosomal subunit protein eL13z
6: RNA (119-MER)
Cm: Ubiquitin-ribosomal protein eL40z fusion protein
CZ: Large ribosomal subunit protein eL27x
CM: Large ribosomal subunit protein eL14z
7: RNA (151-MER)
CN: Large ribosomal subunit protein eL15y
Ca: Large ribosomal subunit protein uL15x
w: Large ribosomal subunit protein eL22z
Cb: 60S ribosomal protein L29
CO: Large ribosomal subunit protein uL13w
CB: Large ribosomal subunit protein uL3z
CP: Large ribosomal subunit protein uL22z
Cc: Large ribosomal subunit protein eL30x
CQ: Large ribosomal subunit protein eL18y
CC: Large ribosomal subunit protein uL4z
CR: Large ribosomal subunit protein eL19z
Cd: Large ribosomal subunit protein eL31x
CS: Ribosomal protein L18ae/LX family protein
CD: Large ribosomal subunit protein uL18z
CT: Large ribosomal subunit protein eL21x/eL21w
Ce: Large ribosomal subunit protein eL32z
CV: Large ribosomal subunit protein uL14x/uL14z/uL14y
CE: Large ribosomal subunit protein eL6x
CW: Large ribosomal subunit protein eL24z
Cf: Large ribosomal subunit protein eL33z
CX: Large ribosomal subunit protein uL23y
CF: Large ribosomal subunit protein uL30y
Cg: Large ribosomal subunit protein eL34z
CG: Large ribosomal subunit protein eL8z
Ch: Large ribosomal subunit protein uL29x
CH: Large ribosomal subunit protein uL6z/uL6y
Ci: Large ribosomal subunit protein eL36y
CI: Large ribosomal subunit protein uL16y
Cj: Large ribosomal subunit protein eL37z
CJ: Large ribosomal subunit protein uL5z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,970,32094
Polymers1,968,77343
Non-polymers1,54751
Water00
1


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

-
Components

-
RNA chain , 3 types, 3 molecules 567

#1: RNA chain 25S RNA


Mass: 1094756.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
#9: RNA chain RNA (119-MER)


Mass: 38917.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: GenBank: 2442578393
#13: RNA chain RNA (151-MER)


Mass: 52785.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: GenBank: 3019173171

+
Large ribosomal subunit protein ... , 36 types, 36 molecules CkCACKClCYCLCZCMCNCawCOCBCPCcCQCCCRCdCDCTCeCVCECWCfCXCFCgCG...

#2: 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
#3: Protein Large ribosomal subunit protein uL2x / 60S ribosomal protein L8-3


Mass: 28008.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q42064
#4: 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
#6: 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
#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
#8: 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
#11: 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
#12: Protein Large ribosomal subunit protein eL14z / 60S ribosomal protein L14-1


Mass: 15536.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SIM4
#14: Protein Large ribosomal subunit protein eL15y / 60S ribosomal protein L15-2


Mass: 24297.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8VYF1
#15: 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
#16: 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
#18: Protein Large ribosomal subunit protein uL13w / 60S ribosomal protein L13a-4


Mass: 23643.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FKC0
#19: Protein Large ribosomal subunit protein uL3z / 60S ribosomal protein L3-1 / Protein EMBRYO DEFECTIVE 2207


Mass: 44653.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P17094
#20: 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
#21: Protein Large ribosomal subunit protein eL30x / 60S ribosomal protein L30-3


Mass: 12300.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LSA3
#22: Protein Large ribosomal subunit protein eL18y / 60S ribosomal protein L18-2


Mass: 20972.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P42791
#23: 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
#24: Protein Large ribosomal subunit protein eL19z / 60S ribosomal protein L19-2


Mass: 24395.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LUQ6
#25: Protein Large ribosomal subunit protein eL31x / 60S ribosomal protein L31-3


Mass: 13836.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P51420
#27: 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
#28: Protein Large ribosomal subunit protein eL21x/eL21w / 60S ribosomal protein L21-2


Mass: 18749.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FDZ9
#29: 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 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
#31: Protein Large ribosomal subunit protein eL6x / 60S ribosomal protein L6-3


Mass: 26160.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C9C5
#32: 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
#33: Protein Large ribosomal subunit protein eL33z / 60S ribosomal protein L35a-2


Mass: 12823.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FZH0
#34: 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
#35: Protein Large ribosomal subunit protein uL30y / 60S ribosomal protein L7-2


Mass: 28226.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P60040
#36: 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
#37: Protein Large ribosomal subunit protein eL8z / 60S ribosomal protein L7a-1


Mass: 29191.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49692
#38: 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
#39: 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
#40: 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
#41: 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
#42: 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
#43: 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

-
Protein , 4 types, 4 molecules CpCmCbCS

#5: Protein (thale cress) hypothetical protein


Mass: 10356.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A7G2EP20
#10: Protein Ubiquitin-ribosomal protein eL40z fusion protein


Mass: 14763.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: B9DHA6
#17: 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
#26: 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

-
Non-polymers , 3 types, 51 molecules

#44: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: K
#45: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Mg
#46: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 60S LSU Arabidopsis (root) ribosome complex / Type: RIBOSOME
Entity ID: #1, #9, #13, #3, #19, #23, #27, #31, #35, #37, #39, #41, #43, #4, #8, #12, #14, #18, #20, #22, #24, #26, #28, #30, #32, #34, #7, #11, #15, #17, #21, #25, #29, #33, #36, #38, #40, #42, #2, #6, #10, #5, #16
Source: NATURAL
Molecular weightValue: 4.3 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis (plant)
Buffer solutionpH: 7.4
Details: 50 mM Hepes, pH 7.4, 5 mM MgAc, 100 mM KAc, pH 7.5, 1 mM DTT, Complete protease inhibitor
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
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: OTHER
Electron lensMode: OTHER / Nominal magnification: 105000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Image recordingElectron dose: 24.512 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115070 / Symmetry type: POINT
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more