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 

wwPDB Validation 3D Report Full Report


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
  • Structures With Same Primary Citation

  • 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 suggest ...

    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: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6 alpha, chloroplasticf146Spinacia oleraceaMutation(s): 0 
Gene Names: RPS6SOVF_120630
Find proteins for P82403 (Spinacia oleracea)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7, chloroplasticg155Spinacia oleraceaMutation(s): 0 
Gene Names: rps7-Arps7-B
Find proteins for P82129 (Spinacia oleracea)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9, chloroplastici157Spinacia oleraceaMutation(s): 0 
Gene Names: PRPS9SOVF_016530
Find proteins for P82278 (Spinacia oleracea)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S1, chloroplastic8370Spinacia oleraceaMutation(s): 0 
Gene Names: RPS1SOVF_099990
Find proteins for P29344 (Spinacia oleracea)
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2, chloroplasticb236Spinacia oleraceaMutation(s): 0 
Gene Names: rps2
Find proteins for P08242 (Spinacia oleracea)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12, chloroplasticl123Spinacia oleraceaMutation(s): 0 
Gene Names: rps12-Arps12-B
Find proteins for P62128 (Spinacia oleracea)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13, chloroplasticm126Spinacia oleraceaMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15, chloroplastico90Spinacia oleraceaMutation(s): 0 
Gene Names: rps15
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16, chloroplasticp88Spinacia oleraceaMutation(s): 0 
Gene Names: rps16
Find proteins for P28807 (Spinacia oleracea)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
protein S17q108Spinacia oleraceaMutation(s): 0 
Gene Names: RPS17SOVF_042540
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18, chloroplasticr101Spinacia oleraceaMutation(s): 0 
Gene Names: RPS18
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19 alpha, chloroplastics92Spinacia oleraceaMutation(s): 0 
Gene Names: rps19
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
protein S20t108Spinacia oleraceaMutation(s): 0 
Gene Names: RPS20
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
protein S21u137Spinacia oleraceaMutation(s): 0 
Gene Names: rps21SOVF_070750
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
protein plastid pYy236Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP1RPS22RPS30SOVF_177810
Find proteins for P19954 (Spinacia oleracea)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3, chloroplasticc218Spinacia oleraceaMutation(s): 0 
Gene Names: rps3
Find proteins for P09595 (Spinacia oleracea)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
protein cS23w121Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP3SOVF_058240
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4, chloroplasticd201Spinacia oleraceaMutation(s): 0 
Gene Names: rps4
Find proteins for P13788 (Spinacia oleracea)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
protein cS22v198Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP2SOVF_116380
Find proteins for P82277 (Spinacia oleracea)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14, chloroplasticn100Spinacia oleraceaMutation(s): 0 
Gene Names: rps14
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
protein bTHXcx47Spinacia oleraceaMutation(s): 0 
Gene Names: RPS31PSRP4SOVF_048530
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5, chloroplastice253Spinacia oleraceaMutation(s): 0 
Gene Names: rps5SOVF_195380
Find proteins for Q9ST69 (Spinacia oleracea)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8, chloroplastich134Spinacia oleraceaMutation(s): 0 
Gene Names: rps8
Find proteins for P09597 (Spinacia oleracea)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
protein S10j122Spinacia oleraceaMutation(s): 0 
Gene Names: RPS10SOVF_026730
Find proteins for P82162 (Spinacia oleracea)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11, chloroplastick138Spinacia oleraceaMutation(s): 0 
Gene Names: rps11
Find proteins for P06506 (Spinacia oleracea)
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Entity ID: 20
MoleculeChainsLengthOrganism
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 

  • 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