9SDP | pdb_00009sdp

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: TISSUE 
  • Reconstruction Method: SINGLE PARTICLE 

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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: 942.68 kDa 
  • Atom Count: 44,802 
  • Modeled Residue Count: 3,783 
  • Deposited Residue Count: 4,993 
  • Unique protein chains: 19
  • Unique nucleic acid chains: 1

Macromolecules


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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2yB [auth BA]280Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q8H173 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1zC [auth BB]262Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9CAV0 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5wD [auth BC]276Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SCM3 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4zE [auth BE]261Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q93VH9 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS6yF [auth BG]249Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P51430 (Arabidopsis thaliana)
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS7zG [auth BH]191Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9C514 (Arabidopsis thaliana)
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS8zH [auth BI]222Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q93VG5 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4yI [auth BJ]197Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FLF0 (Arabidopsis thaliana)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17zJ [auth BL]160Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P16181 (Arabidopsis thaliana)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15yK [auth BN]151Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P59224 (Arabidopsis thaliana)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11xL [auth cS]150Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P42036 (Arabidopsis thaliana)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21zM [auth BV]82Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9M337 (Arabidopsis thaliana)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8z/uS8wN [auth BW]130Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P42798 (Arabidopsis thaliana)
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12yO [auth BX]142Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P49201 (Arabidopsis thaliana)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS24zP [auth BY]133Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SS17 (Arabidopsis thaliana)
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS26xQ [auth BZ]130Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9LYK9 (Arabidopsis thaliana)
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27yR [auth Bb]86Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9M2F1 (Arabidopsis thaliana)
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS30z/eS30y/eS30xS [auth Be]62Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P49689 (Arabidopsis thaliana)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32vT [auth Cn]25Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P62120 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S RNAA [auth 9]1,804Arabidopsis thaliana
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
LA [auth BZ]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
(Subject of Investigation/LOI)

Query on K



Download:Ideal Coordinates CCD File
U [auth 9],
V [auth 9],
W [auth 9]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
AA [auth 9]
BA [auth 9]
CA [auth 9]
DA [auth 9]
EA [auth 9]
AA [auth 9],
BA [auth 9],
CA [auth 9],
DA [auth 9],
EA [auth 9],
FA [auth 9],
GA [auth 9],
HA [auth 9],
IA [auth 9],
JA [auth 9],
KA [auth 9],
X [auth 9],
Y [auth 9],
Z [auth 9]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: TISSUE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

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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 and 314672

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