9SCU | pdb_00009scu

Cryo-EM structure of the Arabidopsis thaliana 60S ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: TISSUE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9SCU

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: 1,970.32 kDa 
  • Atom Count: 118,119 
  • Modeled Residue Count: 9,331 
  • Deposited Residue Count: 10,514 
  • Unique protein chains: 40
  • Unique nucleic acid chains: 3

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL38z/eL38yB [auth Ck]69Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for O22860 (Arabidopsis thaliana)
Explore O22860 
Go to UniProtKB:  O22860
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO22860
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2xC [auth CA]258Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q42064 (Arabidopsis thaliana)
Explore Q42064 
Go to UniProtKB:  Q42064
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ42064
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42z/eL42yD [auth CK]105Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for O23290 (Arabidopsis thaliana)
Explore O23290 
Go to UniProtKB:  O23290
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO23290
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
(thale cress) hypothetical proteinE [auth Cp]92Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for A0A7G2EP20 (Arabidopsis thaliana)
Explore A0A7G2EP20 
Go to UniProtKB:  A0A7G2EP20
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7G2EP20
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL39z/eL39xF [auth Cl]51Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P51424 (Arabidopsis thaliana)
Explore P51424 
Go to UniProtKB:  P51424
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51424
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24zG [auth CY]146Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P51414 (Arabidopsis thaliana)
Explore P51414 
Go to UniProtKB:  P51414
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51414
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13zH [auth CL]206Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P41127 (Arabidopsis thaliana)
Explore P41127 
Go to UniProtKB:  P41127
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41127
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-ribosomal protein eL40z fusion proteinJ [auth Cm]128Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for B9DHA6 (Arabidopsis thaliana)
Explore B9DHA6 
Go to UniProtKB:  B9DHA6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9DHA6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL27xK [auth CZ]135Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P51419 (Arabidopsis thaliana)
Explore P51419 
Go to UniProtKB:  P51419
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51419
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL14zL [auth CM]134Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SIM4 (Arabidopsis thaliana)
Explore Q9SIM4 
Go to UniProtKB:  Q9SIM4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SIM4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL15yN [auth CN]204Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q8VYF1 (Arabidopsis thaliana)
Explore Q8VYF1 
Go to UniProtKB:  Q8VYF1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VYF1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15xO [auth Ca]146Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P49637 (Arabidopsis thaliana)
Explore P49637 
Go to UniProtKB:  P49637
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49637
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22zP [auth w]124Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9M9W1 (Arabidopsis thaliana)
Explore Q9M9W1 
Go to UniProtKB:  Q9M9W1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M9W1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L29Q [auth Cb]83Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for F4JC32 (Arabidopsis thaliana)
Explore F4JC32 
Go to UniProtKB:  F4JC32
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4JC32
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13wR [auth CO]206Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FKC0 (Arabidopsis thaliana)
Explore Q9FKC0 
Go to UniProtKB:  Q9FKC0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FKC0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3zS [auth CB]389Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P17094 (Arabidopsis thaliana)
Explore P17094 
Go to UniProtKB:  P17094
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17094
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22zT [auth CP]176Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q93VI3 (Arabidopsis thaliana)
Explore Q93VI3 
Go to UniProtKB:  Q93VI3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93VI3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30xU [auth Cc]112Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9LSA3 (Arabidopsis thaliana)
Explore Q9LSA3 
Go to UniProtKB:  Q9LSA3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LSA3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18yV [auth CQ]187Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P42791 (Arabidopsis thaliana)
Explore P42791 
Go to UniProtKB:  P42791
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42791
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4zW [auth CC]406Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SF40 (Arabidopsis thaliana)
Explore Q9SF40 
Go to UniProtKB:  Q9SF40
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SF40
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL19zX [auth CR]209Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9LUQ6 (Arabidopsis thaliana)
Explore Q9LUQ6 
Go to UniProtKB:  Q9LUQ6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LUQ6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL31xY [auth Cd]119Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P51420 (Arabidopsis thaliana)
Explore P51420 
Go to UniProtKB:  P51420
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51420
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein L18ae/LX family proteinZ [auth CS]217Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for A0A1P8AY36 (Arabidopsis thaliana)
Explore A0A1P8AY36 
Go to UniProtKB:  A0A1P8AY36
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1P8AY36
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18zAA [auth CD]301Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q8LBI1 (Arabidopsis thaliana)
Explore Q8LBI1 
Go to UniProtKB:  Q8LBI1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8LBI1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL21x/eL21wBA [auth CT]164Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FDZ9 (Arabidopsis thaliana)
Explore Q9FDZ9 
Go to UniProtKB:  Q9FDZ9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FDZ9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32zCA [auth Ce]133Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P49211 (Arabidopsis thaliana)
Explore P49211 
Go to UniProtKB:  P49211
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49211
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14x/uL14z/uL14yDA [auth CV]140Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P49690 (Arabidopsis thaliana)
Explore P49690 
Go to UniProtKB:  P49690
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49690
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6xEA [auth CE]233Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9C9C5 (Arabidopsis thaliana)
Explore Q9C9C5 
Go to UniProtKB:  Q9C9C5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C9C5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL24zFA [auth CW]164Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q42347 (Arabidopsis thaliana)
Explore Q42347 
Go to UniProtKB:  Q42347
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ42347
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33zGA [auth Cf]111Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9FZH0 (Arabidopsis thaliana)
Explore Q9FZH0 
Go to UniProtKB:  Q9FZH0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FZH0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23yHA [auth CX]154Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9M3C3 (Arabidopsis thaliana)
Explore Q9M3C3 
Go to UniProtKB:  Q9M3C3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M3C3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30yIA [auth CF]242Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P60040 (Arabidopsis thaliana)
Explore P60040 
Go to UniProtKB:  P60040
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60040
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34zJA [auth Cg]120Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q42351 (Arabidopsis thaliana)
Explore Q42351 
Go to UniProtKB:  Q42351
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ42351
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8zKA [auth CG]257Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P49692 (Arabidopsis thaliana)
Explore P49692 
Go to UniProtKB:  P49692
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49692
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29xLA [auth Ch]123Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9M3D2 (Arabidopsis thaliana)
Explore Q9M3D2 
Go to UniProtKB:  Q9M3D2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M3D2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6z/uL6yMA [auth CH]194Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P49209 (Arabidopsis thaliana)
Explore P49209 
Go to UniProtKB:  P49209
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49209
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL36yNA [auth Ci]112Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9M352 (Arabidopsis thaliana)
Explore Q9M352 
Go to UniProtKB:  Q9M352
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M352
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16yOA [auth CI]221Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q08770 (Arabidopsis thaliana)
Explore Q08770 
Go to UniProtKB:  Q08770
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08770
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37zPA [auth Cj]95Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q8LFH7 (Arabidopsis thaliana)
Explore Q8LFH7 
Go to UniProtKB:  Q8LFH7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8LFH7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5zQA [auth CJ]182Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P42795 (Arabidopsis thaliana)
Explore P42795 
Go to UniProtKB:  P42795
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42795
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
25S RNAA [auth 5]3,381Arabidopsis thaliana
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 9
MoleculeChains LengthOrganismImage
RNA (119-MER)I [auth 6]121Arabidopsis thaliana
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 13
MoleculeChains LengthOrganismImage
RNA (151-MER)M [auth 7]164Arabidopsis thaliana
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
PC [auth Cp]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
AB [auth 5]
BB [auth 5]
CB [auth 5]
DB [auth 5]
EB [auth 5]
AB [auth 5],
BB [auth 5],
CB [auth 5],
DB [auth 5],
EB [auth 5],
FB [auth 5],
GB [auth 5],
HB [auth 5],
IB [auth 5],
RA [auth 5],
SA [auth 5],
TA [auth 5],
UA [auth 5],
VA [auth 5],
WA [auth 5],
XA [auth 5],
YA [auth 5],
ZA [auth 5]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AC [auth 5]
BC [auth 5]
CC [auth 5]
DC [auth 5]
EC [auth 5]
AC [auth 5],
BC [auth 5],
CC [auth 5],
DC [auth 5],
EC [auth 5],
FC [auth 5],
GC [auth 5],
HC [auth 5],
IC [auth 5],
JB [auth 5],
JC [auth 5],
KB [auth 5],
KC [auth 5],
LB [auth 5],
LC [auth 5],
MB [auth 5],
MC [auth 5],
NB [auth 5],
NC [auth 5],
OB [auth 5],
OC [auth 5],
PB [auth 5],
QB [auth 5],
RB [auth 5],
SB [auth 5],
TB [auth 5],
UB [auth 5],
VB [auth 5],
WB [auth 5],
XB [auth 5],
YB [auth 5],
ZB [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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 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