9SDQ | pdb_00009sdq

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

PDB DOI: https://doi.org/10.2210/pdb9SDQ/pdb
EM Map EMD-54790: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Arabidopsis thaliana
Mutation(s): No

Deposited: 2025-08-14 Released: 2026-06-10
Deposition Author(s): Sudeep, K., 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 Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Academy of Finland

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Sudeep, K., Paavilainen, V.O.

To be published.

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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS3z	B [auth BD]	250	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9SIP7 (Arabidopsis thaliana) Explore Q9SIP7 Go to UniProtKB: Q9SIP7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SIP7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS7z	C [auth BF]	207	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9ZUT9 (Arabidopsis thaliana) Explore Q9ZUT9 Go to UniProtKB: Q9ZUT9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZUT9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS19x	D [auth BP]	152	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9FY64 (Arabidopsis thaliana) Explore Q9FY64 Go to UniProtKB: Q9FY64
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9FY64
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS9z	E [auth BQ]	146	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9SK22 (Arabidopsis thaliana) Explore Q9SK22 Go to UniProtKB: Q9SK22
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SK22
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS13z/uS13y/uS13x	F [auth BS]	152	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P34788 (Arabidopsis thaliana) Explore P34788 Go to UniProtKB: P34788
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34788
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS19x	G [auth BT]	142	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9FNP8 (Arabidopsis thaliana) Explore Q9FNP8 Go to UniProtKB: Q9FNP8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9FNP8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS10z/uS10x	H [auth BU]	124	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P49200 (Arabidopsis thaliana) Explore P49200 Go to UniProtKB: P49200
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49200
Sequence Annotations Expand
Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS28x	I [auth Bc]	64	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P34789 (Arabidopsis thaliana) Explore P34789 Go to UniProtKB: P34789
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34789
Sequence Annotations Expand
Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS14z/uS14y/uS14x	J [auth d]	56	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q680P8 (Arabidopsis thaliana) Explore Q680P8 Go to UniProtKB: Q680P8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q680P8
Sequence Annotations Expand
Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS25y	K [auth e]	108	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9SIK2 (Arabidopsis thaliana) Explore Q9SIK2 Go to UniProtKB: Q9SIK2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SIK2
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS10x	L [auth BK]	179	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9LTF2 (Arabidopsis thaliana) Explore Q9LTF2 Go to UniProtKB: Q9LTF2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LTF2
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Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS17w	M [auth BR]	141	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9LZ17 (Arabidopsis thaliana) Explore Q9LZ17 Go to UniProtKB: Q9LZ17
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LZ17
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
RNA (500-MER)	A [auth 2]	498	Arabidopsis thaliana
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain R [auth d] MOL2 format, chain R [auth d] mmCIF format, chain R [auth d]	R [auth d]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain R [auth d] Interactions & Density Focus chain R [auth d]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain N [auth 2] SDF format, chain O [auth 2] SDF format, chain P [auth 2] MOL2 format, chain N [auth 2] MOL2 format, chain O [auth 2] MOL2 format, chain P [auth 2] mmCIF format, chain N [auth 2] mmCIF format, chain O [auth 2] mmCIF format, chain P [auth 2]	N [auth 2], O [auth 2], P [auth 2]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain N [auth 2] Focus chain O [auth 2] Focus chain P [auth 2] Interactions & Density Focus chain N [auth 2] Focus chain O [auth 2] Focus chain P [auth 2]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth 2] MOL2 format, chain Q [auth 2] mmCIF format, chain Q [auth 2]	Q [auth 2]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth 2] Interactions & Density Focus chain Q [auth 2]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM132649[PVO1]
Academy of Finland	Finland	338836
Academy of Finland	Finland	314672

Revision History (Full details and data files)

Version 1.0: 2026-06-10
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9SDQ | pdb_00009sdq

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

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 1

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)