9SDQ | pdb_00009sdq

Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit (Head)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: TISSUE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9SDQ

This is version 1.1 of the entry. See complete history

Literature

Cryo-EM structure of the Arabidopsisthaliana ribosome in translating and non-translating states.

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.

(2026) Structure 

  • DOI: https://doi.org/10.1016/j.str.2026.06.001
  • Primary Citation Related Structures: 
    9SCU, 9SDP, 9SDQ

  • PubMed 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 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.


  • Organizational Affiliation
    • Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, 00014 Helsinki, Finland; Onego Bio, Hämeentie 157, 00560 Helsinki, Finland.

Macromolecule Content 

  • Total Structure Weight: 353.71 kDa 
  • Atom Count: 21,462 
  • Modeled Residue Count: 1,856 
  • Deposited Residue Count: 2,219 
  • Unique protein chains: 12
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3zB [auth BD]250Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SIP7 (Arabidopsis thaliana)
Explore Q9SIP7 
Go to UniProtKB:  Q9SIP7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SIP7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7zC [auth BF]207Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9ZUT9 (Arabidopsis thaliana)
Explore Q9ZUT9 
Go to UniProtKB:  Q9ZUT9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZUT9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19xD [auth BP]152Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FY64 (Arabidopsis thaliana)
Explore Q9FY64 
Go to UniProtKB:  Q9FY64
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FY64
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9zE [auth BQ]146Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SK22 (Arabidopsis thaliana)
Explore Q9SK22 
Go to UniProtKB:  Q9SK22
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SK22
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13z/uS13y/uS13xF [auth BS]152Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P34788 (Arabidopsis thaliana)
Explore P34788 
Go to UniProtKB:  P34788
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34788
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19xG [auth BT]142Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FNP8 (Arabidopsis thaliana)
Explore Q9FNP8 
Go to UniProtKB:  Q9FNP8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FNP8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10z/uS10xH [auth BU]124Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P49200 (Arabidopsis thaliana)
Explore P49200 
Go to UniProtKB:  P49200
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49200
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS28xI [auth Bc]64Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P34789 (Arabidopsis thaliana)
Explore P34789 
Go to UniProtKB:  P34789
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34789
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14z/uS14y/uS14xJ [auth d]56Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q680P8 (Arabidopsis thaliana)
Explore Q680P8 
Go to UniProtKB:  Q680P8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ680P8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS25yK [auth e]108Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SIK2 (Arabidopsis thaliana)
Explore Q9SIK2 
Go to UniProtKB:  Q9SIK2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SIK2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS10xL [auth BK]179Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9LTF2 (Arabidopsis thaliana)
Explore Q9LTF2 
Go to UniProtKB:  Q9LTF2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LTF2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17wM [auth BR]141Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9LZ17 (Arabidopsis thaliana)
Explore Q9LZ17 
Go to UniProtKB:  Q9LZ17
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LZ17
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (500-MER)A [auth 2]498Arabidopsis thaliana
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: TISSUE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM132649[PVO1]
Academy of FinlandFinland338836
Academy of FinlandFinland314672

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-10
    Type: Initial release
  • Version 1.1: 2026-07-08
    Changes: Data collection, Database references