5X8P

Structure of the 70S chloroplast ribosome from spinach


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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: 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32, chloroplasticA [auth 1]56Spinacia oleraceaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33, chloroplasticB [auth 2]65Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34, chloroplasticC [auth 3]61Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35, chloroplasticD [auth 4]73Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36, chloroplasticE [auth 5]37Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
protein cL37F [auth 6]142Spinacia oleraceaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
protein cL38G [auth 7]116Spinacia oleraceaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2, chloroplasticI [auth C]271Spinacia oleraceaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
protein L3J [auth D]221Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4, chloroplasticK [auth E]243Spinacia oleraceaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5, chloroplasticL [auth F]220Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
protein L6M [auth G]182Spinacia oleraceaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
protein L9N [auth H]155Spinacia oleraceaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13, chloroplasticO [auth K]197Spinacia oleraceaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14, chloroplasticP [auth L]121Spinacia oleraceaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
protein L15Q [auth M]192Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16, chloroplasticR [auth N]135Spinacia oleraceaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
protein L17S [auth O]116Spinacia oleraceaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
protein L18T [auth P]123Spinacia oleraceaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19, chloroplasticU [auth Q]156Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20, chloroplasticV [auth R]127Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21, chloroplasticW [auth S]201Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22, chloroplasticX [auth T]199Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23, chloroplasticY [auth U]122Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24, chloroplasticZ [auth V]145Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
protein L27BA [auth X]137Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
protein L28CA [auth Y]77Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
protein L29DA [auth Z]109Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31FA [auth 0]94Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2, chloroplasticGA [auth b]236Spinacia oleraceaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3, chloroplasticHA [auth c]218Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5, chloroplasticIA [auth e]253Spinacia oleraceaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6 alpha, chloroplasticJA [auth f]146Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7, chloroplasticKA [auth g]155Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8, chloroplasticLA [auth h]134Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9, chloroplasticMA [auth i]157Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
protein S10NA [auth j]122Spinacia oleraceaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11, chloroplasticOA [auth k]138Spinacia oleraceaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12, chloroplasticPA [auth l]123Spinacia oleraceaMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13, chloroplasticQA [auth m]126Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15, chloroplasticRA [auth o]90Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16, chloroplasticSA [auth p]88Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
protein S17TA [auth q]108Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18, chloroplasticUA [auth r]101Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19 alpha, chloroplasticVA [auth s]92Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
protein S20WA [auth t]108Spinacia oleraceaMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
protein S21XA [auth u]137Spinacia oleraceaMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
protein plastid pYYA [auth y]236Spinacia oleraceaMutation(s): 0 
UniProt
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UniProt GroupP19954
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
protein cS23AB [auth w]121Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82412 (Spinacia oleracea)
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UniProt GroupP82412
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4, chloroplasticBB [auth d]201Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P13788 (Spinacia oleracea)
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UniProt GroupP13788
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
protein cS22CB [auth v]198Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P82277 (Spinacia oleracea)
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UniProt GroupP82277
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14, chloroplasticDB [auth n]100Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P06507 (Spinacia oleracea)
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UniProt GroupP06507
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
protein bTHXcEB [auth x]47Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P47910 (Spinacia oleracea)
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UniProt GroupP47910
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1, chloroplasticFB [auth 8]370Spinacia oleraceaMutation(s): 0 
UniProt
Find proteins for P29344 (Spinacia oleracea)
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UniProt GroupP29344
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Entity ID: 8
MoleculeChains LengthOrganismImage
5S rRNAH [auth B]121Spinacia oleracea
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Entity ID: 27
MoleculeChains LengthOrganismImage
4.8S rRNAAA [auth W]106Spinacia oleracea
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Entity ID: 31
MoleculeChains LengthOrganismImage
23S rRNAEA [auth A]2,810Spinacia oleracea
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Entity ID: 52
MoleculeChains LengthOrganismImage
16S rRNAZA [auth a]1,491Spinacia oleracea
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

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