5X8R

Structure of the 30S small subunit of chloroplast ribosome from spinach


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.4 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: 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 ...

    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

    NTU Institute of Structural Biology, Nanyang Technological University, 639798, Singapore.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2, chloroplastic b236Spinacia oleraceaMutation(s): 0 
Gene Names: rps2
Find proteins for P08242 (Spinacia oleracea)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3, chloroplastic c218Spinacia oleraceaMutation(s): 0 
Gene Names: rps3
Find proteins for P09595 (Spinacia oleracea)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5, chloroplastic e253Spinacia oleraceaMutation(s): 0 
Gene Names: rps5SOVF_195380
Find proteins for Q9ST69 (Spinacia oleracea)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6 alpha, chloroplastic f146Spinacia oleraceaMutation(s): 0 
Gene Names: RPS6SOVF_120630
Find proteins for P82403 (Spinacia oleracea)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7, chloroplastic g155Spinacia oleraceaMutation(s): 0 
Gene Names: rps7-Arps7-B
Find proteins for P82129 (Spinacia oleracea)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8, chloroplastic h134Spinacia oleraceaMutation(s): 0 
Gene Names: rps8
Find proteins for P09597 (Spinacia oleracea)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9, chloroplastic i157Spinacia oleraceaMutation(s): 0 
Gene Names: PRPS9SOVF_016530
Find proteins for P82278 (Spinacia oleracea)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
protein S10 j122Spinacia oleraceaMutation(s): 0 
Gene Names: RPS10SOVF_026730
Find proteins for P82162 (Spinacia oleracea)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11, chloroplastic k138Spinacia oleraceaMutation(s): 0 
Gene Names: rps11
Find proteins for P06506 (Spinacia oleracea)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12, chloroplastic l123Spinacia oleraceaMutation(s): 0 
Gene Names: rps12-Arps12-B
Find proteins for P62128 (Spinacia oleracea)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13, chloroplastic m126Spinacia oleraceaMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15, chloroplastic o90Spinacia oleraceaMutation(s): 0 
Gene Names: rps15
Find proteins for Q9M3I4 (Spinacia oleracea)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16, chloroplastic p88Spinacia oleraceaMutation(s): 0 
Gene Names: rps16
Find proteins for P28807 (Spinacia oleracea)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
protein S17 q108Spinacia oleraceaMutation(s): 0 
Gene Names: RPS17SOVF_042540
Find proteins for P82137 (Spinacia oleracea)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18, chloroplastic r101Spinacia oleraceaMutation(s): 0 
Gene Names: RPS18
Find proteins for Q9M3K7 (Spinacia oleracea)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19 alpha, chloroplastic s92Spinacia oleraceaMutation(s): 0 
Gene Names: rps19
Find proteins for P06508 (Spinacia oleracea)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
protein S20 t108Spinacia oleraceaMutation(s): 0 
Gene Names: RPS20
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
protein S21 u137Spinacia oleraceaMutation(s): 0 
Gene Names: rps21SOVF_070750
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
protein plastid pY y236Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP1RPS22RPS30SOVF_177810
Find proteins for P19954 (Spinacia oleracea)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
protein cS23 w121Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP3SOVF_058240
Find proteins for P82412 (Spinacia oleracea)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4, chloroplastic d201Spinacia oleraceaMutation(s): 0 
Gene Names: rps4
Find proteins for P13788 (Spinacia oleracea)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
protein cS22 v198Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP2SOVF_116380
Find proteins for P82277 (Spinacia oleracea)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14, chloroplastic n100Spinacia oleraceaMutation(s): 0 
Gene Names: rps14
Find proteins for P06507 (Spinacia oleracea)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
protein bTHXc x47Spinacia oleraceaMutation(s): 0 
Gene Names: RPS31PSRP4SOVF_048530
Find proteins for P47910 (Spinacia oleracea)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S1, chloroplastic 8370Spinacia oleraceaMutation(s): 0 
Gene Names: RPS1SOVF_099990
Find proteins for P29344 (Spinacia oleracea)
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Entity ID: 20
MoleculeChainsLengthOrganismImage
16S rRNAa1491Spinacia oleracea
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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