5X8T

Structure of the 50S large subunit of chloroplast ribosome from spinach


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation

Ahmed, T.Shi, J.Bhushan, S.

(2017) Nucleic Acids Res 45: 8581-8595

  • DOI: https://doi.org/10.1093/nar/gkx499
  • Primary Citation of Related Structures:  
    5X8P, 5X8R, 5X8T

  • PubMed Abstract: 

    Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggested to play important regulatory roles in translation. However, their exact locations on the chloroplast ribosome remain elusive due to lack of a high-resolution structure, hindering our progress to understand their possible roles. Here we present a cryo-EM structure of the 70S chloroplast ribosome from spinach resolved to 3.4 Å and focus our discussion mainly on the architecture of the 30S small subunit (SSU) which is resolved to 3.7 Å. cS22 localizes at the SSU foot where it seems to compensate for the deletions in 16S rRNA. The mRNA exit site is highly remodeled due to the presence of cS23 suggesting an alternative mode of translation initiation. bTHXc is positioned at the SSU head and appears to stabilize the intersubunit bridge B1b during thermal fluctuations. The translation factor plastid pY binds to the SSU on the intersubunit side and interacts with the conserved nucleotide bases involved in decoding. Most of the intersubunit bridges are conserved compared to the bacteria, except for a new bridge involving uL2c and bS6c.


  • Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, 637551, Singapore.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32, chloroplasticA [auth 1]56Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P28804 (Spinacia oleracea)
Explore P28804 
Go to UniProtKB:  P28804
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28804
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33, chloroplasticB [auth 2]65Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P28805 (Spinacia oleracea)
Explore P28805 
Go to UniProtKB:  P28805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28805
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34, chloroplasticC [auth 3]61Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82244 (Spinacia oleracea)
Explore P82244 
Go to UniProtKB:  P82244
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82244
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35, chloroplasticD [auth 4]73Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P23326 (Spinacia oleracea)
Explore P23326 
Go to UniProtKB:  P23326
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23326
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36, chloroplasticE [auth 5]37Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P12230 (Spinacia oleracea)
Explore P12230 
Go to UniProtKB:  P12230
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12230
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
protein cL37F [auth 6]142Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P27684 (Spinacia oleracea)
Explore P27684 
Go to UniProtKB:  P27684
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27684
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
protein cL38G [auth 7]116Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82411 (Spinacia oleracea)
Explore P82411 
Go to UniProtKB:  P82411
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82411
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2, chloroplasticI [auth C]271Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P06509 (Spinacia oleracea)
Explore P06509 
Go to UniProtKB:  P06509
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06509
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
protein L3J [auth D]221Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82191 (Spinacia oleracea)
Explore P82191 
Go to UniProtKB:  P82191
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82191
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4, chloroplasticK [auth E]243Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for O49937 (Spinacia oleracea)
Explore O49937 
Go to UniProtKB:  O49937
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO49937
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5, chloroplasticL [auth F]220Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82192 (Spinacia oleracea)
Explore P82192 
Go to UniProtKB:  P82192
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82192
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
protein L6M [auth G]182Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82193 (Spinacia oleracea)
Explore P82193 
Go to UniProtKB:  P82193
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82193
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
protein L9N [auth H]155Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82180 (Spinacia oleracea)
Explore P82180 
Go to UniProtKB:  P82180
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82180
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13, chloroplasticO [auth K]197Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P12629 (Spinacia oleracea)
Explore P12629 
Go to UniProtKB:  P12629
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12629
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14, chloroplasticP [auth L]121Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P09596 (Spinacia oleracea)
Explore P09596 
Go to UniProtKB:  P09596
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09596
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
protein L15Q [auth M]192Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P22798 (Spinacia oleracea)
Explore P22798 
Go to UniProtKB:  P22798
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22798
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16, chloroplasticR [auth N]135Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P17353 (Spinacia oleracea)
Explore P17353 
Go to UniProtKB:  P17353
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17353
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
protein L17S [auth O]116Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82194 (Spinacia oleracea)
Explore P82194 
Go to UniProtKB:  P82194
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82194
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
protein L18T [auth P]123Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82195 (Spinacia oleracea)
Explore P82195 
Go to UniProtKB:  P82195
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82195
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19, chloroplasticU [auth Q]156Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82413 (Spinacia oleracea)
Explore P82413 
Go to UniProtKB:  P82413
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82413
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20, chloroplasticV [auth R]127Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P28803 (Spinacia oleracea)
Explore P28803 
Go to UniProtKB:  P28803
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28803
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21, chloroplasticW [auth S]201Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P24613 (Spinacia oleracea)
Explore P24613 
Go to UniProtKB:  P24613
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24613
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22, chloroplasticX [auth T]199Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P09594 (Spinacia oleracea)
Explore P09594 
Go to UniProtKB:  P09594
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09594
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23, chloroplasticY [auth U]122Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for Q9LWB5 (Spinacia oleracea)
Explore Q9LWB5 
Go to UniProtKB:  Q9LWB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LWB5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24, chloroplasticZ [auth V]145Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P27683 (Spinacia oleracea)
Explore P27683 
Go to UniProtKB:  P27683
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27683
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
protein L27BA [auth X]137Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82190 (Spinacia oleracea)
Explore P82190 
Go to UniProtKB:  P82190
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82190
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
protein L28CA [auth Y]77Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82245 (Spinacia oleracea)
Explore P82245 
Go to UniProtKB:  P82245
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82245
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
protein L29DA [auth Z]109Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82248 (Spinacia oleracea)
Explore P82248 
Go to UniProtKB:  P82248
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82248
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31FA [auth 0]94Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82249 (Spinacia oleracea)
Explore P82249 
Go to UniProtKB:  P82249
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82249
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains LengthOrganismImage
5S rRNAH [auth B]121Spinacia oleracea
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains LengthOrganismImage
4.8S rRNAAA [auth W]106Spinacia oleracea
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains LengthOrganismImage
23S rRNAEA [auth A]2,810Spinacia oleracea
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MOESingaporeAcRF Tier 1, 2014-T1-001-019 (RG32/14)

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Database references
  • Version 1.3: 2018-06-06
    Changes: Data collection
  • Version 1.4: 2019-10-16
    Changes: Data collection, Other
  • Version 1.5: 2024-03-27
    Changes: Data collection, Database references