5MLC

Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.5 of the entry. See complete history


Literature

Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions.

Graf, M.Arenz, S.Huter, P.Donhofer, A.Novacek, J.Wilson, D.N.

(2017) Nucleic Acids Res 45: 2887-2896

  • DOI: https://doi.org/10.1093/nar/gkw1272
  • Primary Citation of Related Structures:  
    5MLC

  • PubMed Abstract: 
  • Ribosomes are the protein synthesizing machines of the cell. Recent advances in cryo-EM have led to the determination of structures from a variety of species, including bacterial 70S and eukaryotic 80S ribosomes as well as mitoribosomes from eukaryotic mitochondria, however, to date high resolution structures of plastid 70S ribosomes have been lacking ...

    Ribosomes are the protein synthesizing machines of the cell. Recent advances in cryo-EM have led to the determination of structures from a variety of species, including bacterial 70S and eukaryotic 80S ribosomes as well as mitoribosomes from eukaryotic mitochondria, however, to date high resolution structures of plastid 70S ribosomes have been lacking. Here we present a cryo-EM structure of the spinach chloroplast 70S ribosome, with an average resolution of 5.4 Å for the small 30S subunit and 3.6 Å for the large 50S ribosomal subunit. The structure reveals the location of the plastid-specific ribosomal proteins (RPs) PSRP1, PSRP4, PSRP5 and PSRP6 as well as the numerous plastid-specific extensions of the RPs. We discover many features by which the plastid-specific extensions stabilize the ribosome via establishing additional interactions with surrounding ribosomal RNA and RPs. Moreover, we identify a large conglomerate of plastid-specific protein mass adjacent to the tunnel exit site that could facilitate interaction of the chloroplast ribosome with the thylakoid membrane and the protein-targeting machinery. Comparing the Escherichia coli 70S ribosome with that of the spinach chloroplast ribosome provides detailed insight into the co-evolution of RP and rRNA.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2, chloroplasticD272Spinacia oleraceaMutation(s): 0 
Gene Names: rpl2-Arpl2-B
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Entity ID: 5
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50S ribosomal protein L3, chloroplasticE305Spinacia oleraceaMutation(s): 0 
Gene Names: RPL3SOVF_195350
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4, chloroplasticF293Spinacia oleraceaMutation(s): 0 
Gene Names: RPL4SOVF_029280
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5, chloroplasticG220Spinacia oleraceaMutation(s): 0 
Gene Names: RPL5PrpL5SOVF_057730
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6, chloroplasticH220Spinacia oleraceaMutation(s): 0 
Gene Names: RPL6SOVF_107200
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Entity ID: 9
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50S ribosomal protein L9, chloroplasticI196Spinacia oleraceaMutation(s): 0 
Gene Names: RPL9SOVF_040960
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Entity ID: 10
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50S ribosomal protein L13, chloroplasticJ [auth L]250Spinacia oleraceaMutation(s): 0 
Gene Names: RPL13SOVF_093170
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Entity ID: 11
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50S ribosomal protein L14, chloroplasticK [auth M]121Spinacia oleraceaMutation(s): 0 
Gene Names: rpl14
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Entity ID: 12
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50S ribosomal protein L15, chloroplasticL [auth N]271Spinacia oleraceaMutation(s): 0 
Gene Names: RPL15SOVF_177460
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Entity ID: 13
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50S ribosomal protein L16, chloroplasticM [auth O]135Spinacia oleraceaMutation(s): 0 
Gene Names: rpl16
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17, chloroplasticN [auth P]126Spinacia oleraceaMutation(s): 0 
Gene Names: RPL17SOVF_059230
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Entity ID: 15
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50S ribosomal protein L18, chloroplasticO [auth Q]166Spinacia oleraceaMutation(s): 0 
Gene Names: RPL18PRPL18SOVF_159210
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Entity ID: 16
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50S ribosomal protein L19, chloroplasticP [auth R]233Spinacia oleraceaMutation(s): 0 
Gene Names: RPL19PRPL19SOVF_150800
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Entity ID: 17
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50S ribosomal protein L20, chloroplasticQ [auth S]128Spinacia oleraceaMutation(s): 0 
Gene Names: rpl20
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Entity ID: 18
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50S ribosomal protein L21, chloroplasticR [auth T]256Spinacia oleraceaMutation(s): 0 
Gene Names: RPL21SOVF_056040
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Entity ID: 19
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50S ribosomal protein L22, chloroplasticS [auth U]199Spinacia oleraceaMutation(s): 0 
Gene Names: rpl22
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Entity ID: 20
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50S ribosomal protein L23, chloroplasticT [auth V]198Spinacia oleraceaMutation(s): 0 
Gene Names: RPL23SOVF_109700
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Entity ID: 21
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50S ribosomal protein L24, chloroplasticU [auth W]191Spinacia oleraceaMutation(s): 0 
Gene Names: RPL24SOVF_183870
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Entity ID: 22
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50S ribosomal protein L27, chloroplasticV [auth X]194Spinacia oleraceaMutation(s): 0 
Gene Names: RPL27SOVF_107450
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Entity ID: 23
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50S ribosomal protein L28, chloroplasticW [auth Y]148Spinacia oleraceaMutation(s): 0 
Gene Names: RPL28SOVF_085320
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Entity ID: 24
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50S ribosomal protein L29, chloroplasticX [auth Z]168Spinacia oleraceaMutation(s): 0 
Gene Names: RPL29SOVF_096810
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Entity ID: 25
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50S ribosomal protein L32, chloroplasticY [auth 2]57Spinacia oleraceaMutation(s): 0 
Gene Names: rpl32
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33, chloroplasticZ [auth 3]66Spinacia oleraceaMutation(s): 0 
Gene Names: rpl33
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34, chloroplasticAA [auth 4]152Spinacia oleraceaMutation(s): 0 
Gene Names: RPL34SOVF_073030
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Entity ID: 28
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50S ribosomal protein L35, chloroplasticBA [auth 5]159Spinacia oleraceaMutation(s): 0 
Gene Names: RPL35SOVF_080710
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Entity ID: 29
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50S ribosomal protein L36, chloroplasticCA [auth 6]37Spinacia oleraceaMutation(s): 0 
Gene Names: rpl36
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-recycling factor, chloroplasticDA [auth 9]271Spinacia oleraceaMutation(s): 0 
Gene Names: RRFFRRHCP
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
PSRP5alpha, chloroplasticEA [auth 7]142Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP5RPL40SOVF_000530
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
PSRP6, chloroplasticFA [auth 8]116Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP6SOVF_082300
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNA, chloroplasticA2,811Spinacia oleracea
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Entity ID: 2
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5S ribosomal RNA, chloroplasticB121Spinacia oleracea
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Entity ID: 3
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4.8S ribosomal RNA, chloroplasticC103Spinacia oleracea
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN9.11

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR-1805
German Research FoundationGermanySPP-1879
German Research FoundationGermanyGRK-1721
iNEXT653706

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.3: 2018-10-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-12-11
    Changes: Other