9SDP | pdb_00009sdp

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

PDB DOI: https://doi.org/10.2210/pdb9SDP/pdb
EM Map EMD-54789: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Arabidopsis thaliana
Mutation(s): Yes

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

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 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 ribosome in translating and non-translating states

Karki, S., Paavilainen, V.

To be published.

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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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS2y	B [auth BA]	280	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q8H173 (Arabidopsis thaliana) Explore Q8H173 Go to UniProtKB: Q8H173
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8H173
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 eS1z	C [auth BB]	262	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9CAV0 (Arabidopsis thaliana) Explore Q9CAV0 Go to UniProtKB: Q9CAV0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CAV0
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 uS5w	D [auth BC]	276	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9SCM3 (Arabidopsis thaliana) Explore Q9SCM3 Go to UniProtKB: Q9SCM3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SCM3
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 eS4z	E [auth BE]	261	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q93VH9 (Arabidopsis thaliana) Explore Q93VH9 Go to UniProtKB: Q93VH9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93VH9
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 eS6y	F [auth BG]	249	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P51430 (Arabidopsis thaliana) Explore P51430 Go to UniProtKB: P51430
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51430
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 eS7z	G [auth BH]	191	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9C514 (Arabidopsis thaliana) Explore Q9C514 Go to UniProtKB: Q9C514
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9C514
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 eS8z	H [auth BI]	222	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q93VG5 (Arabidopsis thaliana) Explore Q93VG5 Go to UniProtKB: Q93VG5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93VG5
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS4y	I [auth BJ]	197	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9FLF0 (Arabidopsis thaliana) Explore Q9FLF0 Go to UniProtKB: Q9FLF0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9FLF0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS17z	J [auth BL]	160	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P16181 (Arabidopsis thaliana) Explore P16181 Go to UniProtKB: P16181
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16181
Sequence Annotations Expand
Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS15y	K [auth BN]	151	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P59224 (Arabidopsis thaliana) Explore P59224 Go to UniProtKB: P59224
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59224
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS11x	L [auth cS]	150	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P42036 (Arabidopsis thaliana) Explore P42036 Go to UniProtKB: P42036
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42036
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS21z	M [auth BV]	82	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9M337 (Arabidopsis thaliana) Explore Q9M337 Go to UniProtKB: Q9M337
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9M337
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS8z/uS8w	N [auth BW]	130	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P42798 (Arabidopsis thaliana) Explore P42798 Go to UniProtKB: P42798
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42798
Sequence Annotations Expand
Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS12y	O [auth BX]	142	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P49201 (Arabidopsis thaliana) Explore P49201 Go to UniProtKB: P49201
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49201
Sequence Annotations Expand
Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS24z	P [auth BY]	133	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9SS17 (Arabidopsis thaliana) Explore Q9SS17 Go to UniProtKB: Q9SS17
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SS17
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS26x	Q [auth BZ]	130	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9LYK9 (Arabidopsis thaliana) Explore Q9LYK9 Go to UniProtKB: Q9LYK9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LYK9
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS27y	R [auth Bb]	86	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9M2F1 (Arabidopsis thaliana) Explore Q9M2F1 Go to UniProtKB: Q9M2F1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9M2F1
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS30z/eS30y/eS30x	S [auth Be]	62	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P49689 (Arabidopsis thaliana) Explore P49689 Go to UniProtKB: P49689
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49689
Sequence Annotations Expand
Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v	T [auth Cn]	25	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P62120 (Arabidopsis thaliana) Explore P62120 Go to UniProtKB: P62120
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62120
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
18S RNA	A [auth 9]	1,804	Arabidopsis thaliana
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain LA [auth BZ] MOL2 format, chain LA [auth BZ] mmCIF format, chain LA [auth BZ]	LA [auth BZ]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain LA [auth BZ] Interactions & Density Focus chain LA [auth BZ]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain W [auth 9] SDF format, chain V [auth 9] SDF format, chain U [auth 9] MOL2 format, chain W [auth 9] MOL2 format, chain V [auth 9] MOL2 format, chain U [auth 9] mmCIF format, chain W [auth 9] mmCIF format, chain V [auth 9] mmCIF format, chain U [auth 9]	U [auth 9], V [auth 9], W [auth 9]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain U [auth 9] Focus chain V [auth 9] Focus chain W [auth 9] Interactions & Density Focus chain U [auth 9] Focus chain V [auth 9] Focus chain W [auth 9]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth 9] SDF format, chain Y [auth 9] SDF format, chain X [auth 9] SDF format, chain KA [auth 9] SDF format, chain JA [auth 9] SDF format, chain IA [auth 9] SDF format, chain HA [auth 9] SDF format, chain GA [auth 9] SDF format, chain FA [auth 9] SDF format, chain EA [auth 9] SDF format, chain DA [auth 9] SDF format, chain CA [auth 9] SDF format, chain BA [auth 9] SDF format, chain AA [auth 9] MOL2 format, chain Z [auth 9] MOL2 format, chain Y [auth 9] MOL2 format, chain X [auth 9] MOL2 format, chain KA [auth 9] MOL2 format, chain JA [auth 9] MOL2 format, chain IA [auth 9] MOL2 format, chain HA [auth 9] MOL2 format, chain GA [auth 9] MOL2 format, chain FA [auth 9] MOL2 format, chain EA [auth 9] MOL2 format, chain DA [auth 9] MOL2 format, chain CA [auth 9] MOL2 format, chain BA [auth 9] MOL2 format, chain AA [auth 9] mmCIF format, chain Z [auth 9] mmCIF format, chain Y [auth 9] mmCIF format, chain X [auth 9] mmCIF format, chain KA [auth 9] mmCIF format, chain JA [auth 9] mmCIF format, chain IA [auth 9] mmCIF format, chain HA [auth 9] mmCIF format, chain GA [auth 9] mmCIF format, chain FA [auth 9] mmCIF format, chain EA [auth 9] mmCIF format, chain DA [auth 9] mmCIF format, chain CA [auth 9] mmCIF format, chain BA [auth 9] mmCIF format, chain AA [auth 9]	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		Interactions Focus chain AA [auth 9] Focus chain BA [auth 9] Focus chain CA [auth 9] Focus chain DA [auth 9] Focus chain EA [auth 9] Focus chain FA [auth 9] Focus chain GA [auth 9] Focus chain HA [auth 9] Focus chain IA [auth 9] Focus chain JA [auth 9] Focus chain KA [auth 9] Focus chain X [auth 9] Focus chain Y [auth 9] Focus chain Z [auth 9] Interactions & Density Focus chain AA [auth 9] Focus chain BA [auth 9] Focus chain CA [auth 9] Focus chain DA [auth 9] Focus chain EA [auth 9] Focus chain FA [auth 9] Focus chain GA [auth 9] Focus chain HA [auth 9] Focus chain IA [auth 9] Focus chain JA [auth 9] Focus chain KA [auth 9] Focus chain X [auth 9] Focus chain Y [auth 9] Focus chain Z [auth 9]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 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

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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 and 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.

9SDP | pdb_00009sdp

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

Literature

Cryo-EM structure of the Arabidopsis thaliana ribosome in translating and non-translating states

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: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt

Entity Groups

Sequence Annotations

Entity ID: 19

UniProt

Entity Groups

Sequence Annotations

Entity ID: 20

UniProt