4V61

Homology model for the Spinach chloroplast 30S subunit fitted to 9.4A cryo-EM map of the 70S chlororibosome.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins

Sharma, M.R.Wilson, D.N.Datta, P.P.Barat, C.Schluenzen, F.Fucini, P.Agrawal, R.K.

(2007) Proc Natl Acad Sci U S A 104: 19315-19320

  • DOI: 10.1073/pnas.0709856104
  • Primary Citation of Related Structures:  
    4V61

  • PubMed Abstract: 
  • Protein synthesis in the chloroplast is carried out by chloroplast ribosomes (chloro-ribosome) and regulated in a light-dependent manner. Chloroplast or plastid ribosomal proteins (PRPs) generally are larger than their bacterial counterparts, and chloro-ribosomes contain additional plastid-specific ribosomal proteins (PSRPs); however, it is unclear to what extent these proteins play structural or regulatory roles during translation ...

    Protein synthesis in the chloroplast is carried out by chloroplast ribosomes (chloro-ribosome) and regulated in a light-dependent manner. Chloroplast or plastid ribosomal proteins (PRPs) generally are larger than their bacterial counterparts, and chloro-ribosomes contain additional plastid-specific ribosomal proteins (PSRPs); however, it is unclear to what extent these proteins play structural or regulatory roles during translation. We have obtained a three-dimensional cryo-EM map of the spinach 70S chloro-ribosome, revealing the overall structural organization to be similar to bacterial ribosomes. Fitting of the conserved portions of the x-ray crystallographic structure of the bacterial 70S ribosome into our cryo-EM map of the chloro-ribosome reveals the positions of PRP extensions and the locations of the PSRPs. Surprisingly, PSRP1 binds in the decoding region of the small (30S) ribosomal subunit, in a manner that would preclude the binding of messenger and transfer RNAs to the ribosome, suggesting that PSRP1 is a translation factor rather than a ribosomal protein. PSRP2 and PSRP3 appear to structurally compensate for missing segments of the 16S rRNA within the 30S subunit, whereas PSRP4 occupies a position buried within the head of the 30S subunit. One of the two PSRPs in the large (50S) ribosomal subunit lies near the tRNA exit site. Furthermore, we find a mass of density corresponding to chloro-ribosome recycling factor; domain II of this factor appears to interact with the flexible C-terminal domain of PSRP1. Our study provides evolutionary insights into the structural and functional roles that the PSRPs play during protein synthesis in chloroplasts.


    Organizational Affiliation

    Laboratory of Structural Pathology, Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA.



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Entity ID: 2
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Ribosomal Protein S2B [auth AB]231Spinacia oleraceaMutation(s): 0 
Gene Names: rps2
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Ribosomal Protein S3C [auth AC]218Spinacia oleraceaMutation(s): 0 
Gene Names: rps3
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Ribosomal Protein S4D [auth AD]201Spinacia oleraceaMutation(s): 0 
Gene Names: rps4
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Entity ID: 5
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Ribosomal Protein S5E [auth AE]308Spinacia oleraceaMutation(s): 0 
Gene Names: rps5SOVF_195380
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Entity ID: 6
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Ribosomal Protein S6F [auth AF]168Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S7G [auth AG]155Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S8H [auth AH]134Spinacia oleraceaMutation(s): 0 
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Entity ID: 9
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Ribosomal Protein S9I [auth AI]197Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S10J [auth AJ]197Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S11K [auth AK]140Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S12L [auth AL]123Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S13M [auth AM]145Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S14N [auth AN]100Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S15O [auth AO]90Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S16P [auth AP]88Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S17Q [auth AQ]142Spinacia oleraceaMutation(s): 0 
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Entity ID: 18
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Ribosomal Protein S18R [auth AR]103Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S19S [auth AS]92Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S20T [auth AT]202Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein S21U [auth AU]190Spinacia oleraceaMutation(s): 0 
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Entity ID: 25
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Ribosomal Protein L1Y [auth BD]352Spinacia oleraceaMutation(s): 0 
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Entity ID: 26
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Ribosomal Protein L2Z [auth BE]269Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein L3AA [auth BF]259Spinacia oleraceaMutation(s): 0 
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Entity ID: 28
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Ribosomal Protein L4BA [auth BG]293Spinacia oleraceaMutation(s): 0 
Gene Names: RPL4SOVF_029280
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Entity ID: 29
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Ribosomal Protein L5CA [auth BH]220Spinacia oleraceaMutation(s): 0 
Gene Names: RPL5PrpL5SOVF_057730
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Ribosomal Protein L6DA [auth BI]223Spinacia oleraceaMutation(s): 0 
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Entity ID: 31
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Ribosomal Protein L9EA [auth BJ]197Spinacia oleraceaMutation(s): 0 
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Entity ID: 32
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Ribosomal Protein L11FA [auth BK]224Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein L13GA [auth BL]250Spinacia oleraceaMutation(s): 0 
Gene Names: RPL13SOVF_093170
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Ribosomal Protein L14HA [auth BM]121Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein L15IA [auth BN]257Spinacia oleraceaMutation(s): 0 
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Entity ID: 36
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Ribosomal Protein L16JA [auth BO]135Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein L17KA [auth BP]205Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein L18LA [auth BQ]161Spinacia oleraceaMutation(s): 0 
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Entity ID: 39
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Ribosomal Protein L19MA [auth BR]233Spinacia oleraceaMutation(s): 0 
Gene Names: RPL19PRPL19SOVF_150800
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Ribosomal Protein L20NA [auth BS]119Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein L21OA [auth BT]257Spinacia oleraceaMutation(s): 0 
Gene Names: RPL21SOVF_056040
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Ribosomal Protein L22PA [auth BU]199Spinacia oleraceaMutation(s): 0 
Gene Names: rpl22
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Ribosomal Protein L23QA [auth BV]198Spinacia oleraceaMutation(s): 0 
Gene Names: RPL23SOVF_109700
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Ribosomal Protein L24RA [auth BW]191Spinacia oleraceaMutation(s): 0 
Gene Names: RPL24SOVF_183870
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Ribosomal Protein L27SA [auth BX]198Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein L28TA [auth BY]151Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein L29UA [auth BZ]173Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein L31VA [auth B1]144Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein L32WA [auth B2]57Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein L33XA [auth B3]66Spinacia oleraceaMutation(s): 0 
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Ribosomal Protein L34YA [auth B4]152Spinacia oleraceaMutation(s): 0 
Gene Names: RPL34SOVF_073030
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Entity ID: 52
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Ribosomal Protein L35ZA [auth B5]159Spinacia oleraceaMutation(s): 0 
Gene Names: RPL35SOVF_080710
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Ribosomal Protein L36AB [auth B6]104Spinacia oleraceaMutation(s): 0 
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Entity ID: 1
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16S rRNAA [auth AA]1491Spinacia oleracea
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Entity ID: 22
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23S rRNAV [auth BA]2810Spinacia oleracea
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Entity ID: 23
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5S rRNAW [auth BB]117Spinacia oleracea
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Entity ID: 24
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4.8S rRNAX [auth BC]103Spinacia oleracea
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-03-25
    Changes: Other
  • Version 1.3: 2019-12-18
    Changes: Data collection, Database references, Other