6ERI

Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.

Boerema, A.P.Aibara, S.Paul, B.Tobiasson, V.Kimanius, D.Forsberg, B.O.Wallden, K.Lindahl, E.Amunts, A.

(2018) Nat Plants 4: 212-217

  • DOI: 10.1038/s41477-018-0129-6
  • Primary Citation of Related Structures:  
    6ERI

  • PubMed Abstract: 
  • Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast ...

    Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome 1,2 . Despite recent structural information 3-6 , some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9-3.1 Å resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes.


    Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden. amunts@scilifelab.se.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2, chloroplastic AC246Spinacia oleraceaMutation(s): 0 
Gene Names: rpl2-Arpl2-B
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3, chloroplastic AD221Spinacia oleraceaMutation(s): 0 
Gene Names: RPL3SOVF_195350
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4, chloroplastic AE212Spinacia oleraceaMutation(s): 0 
Gene Names: RPL4SOVF_029280
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5, chloroplastic AF207Spinacia oleraceaMutation(s): 0 
Gene Names: RPL5PrpL5SOVF_057730
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6, chloroplastic AG172Spinacia oleraceaMutation(s): 0 
Gene Names: RPL6SOVF_107200
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9, chloroplastic AH46Spinacia oleraceaMutation(s): 0 
Gene Names: RPL9SOVF_040960
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Entity ID: 9
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50S ribosomal protein L13, chloroplastic AJ200Spinacia oleraceaMutation(s): 0 
Gene Names: RPL13SOVF_093170
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14, chloroplastic AK121Spinacia oleraceaMutation(s): 0 
Gene Names: rpl14
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15, chloroplastic AL184Spinacia oleraceaMutation(s): 0 
Gene Names: RPL15SOVF_177460
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Entity ID: 12
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50S ribosomal protein L16, chloroplastic AM134Spinacia oleraceaMutation(s): 0 
Gene Names: rpl16
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17, chloroplastic AN116Spinacia oleraceaMutation(s): 0 
Gene Names: RPL17SOVF_059230
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18, chloroplastic AO121Spinacia oleraceaMutation(s): 0 
Gene Names: RPL18PRPL18SOVF_159210
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19, chloroplastic AP118Spinacia oleraceaMutation(s): 0 
Gene Names: RPL19PRPL19SOVF_150800
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20, chloroplastic AQ115Spinacia oleraceaMutation(s): 0 
Gene Names: rpl20
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21, chloroplastic AR165Spinacia oleraceaMutation(s): 0 
Gene Names: RPL21SOVF_056040
Find proteins for P24613 (Spinacia oleracea)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22, chloroplastic AS171Spinacia oleraceaMutation(s): 0 
Gene Names: rpl22
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23, chloroplastic AT92Spinacia oleraceaMutation(s): 0 
Gene Names: RPL23SOVF_109700
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24, chloroplastic AU127Spinacia oleraceaMutation(s): 0 
Gene Names: RPL24SOVF_183870
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27, chloroplastic AW114Spinacia oleraceaMutation(s): 0 
Gene Names: RPL27SOVF_107450
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28, chloroplastic AX76Spinacia oleraceaMutation(s): 0 
Gene Names: RPL28SOVF_085320
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29, chloroplastic AY99Spinacia oleraceaMutation(s): 0 
Gene Names: RPL29SOVF_096810
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31, chloroplastic AZ66Spinacia oleraceaMutation(s): 0 
Gene Names: RPL31SOVF_125040
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32, chloroplastic Aa48Spinacia oleraceaMutation(s): 0 
Gene Names: rpl32
Find proteins for P28804 (Spinacia oleracea)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33, chloroplastic Ab60Spinacia oleraceaMutation(s): 0 
Gene Names: rpl33
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34, chloroplastic Ac61Spinacia oleraceaMutation(s): 0 
Gene Names: RPL34SOVF_073030
Find proteins for P82244 (Spinacia oleracea)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35, chloroplastic Ad72Spinacia oleraceaMutation(s): 0 
Gene Names: RPL35SOVF_080710
Find proteins for P23326 (Spinacia oleracea)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36, chloroplastic Ae37Spinacia oleraceaMutation(s): 0 
Gene Names: rpl36
Find proteins for P12230 (Spinacia oleracea)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein 6, chloroplastic Af47Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP6SOVF_082300
Find proteins for P82411 (Spinacia oleracea)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein 5 alpha, chloroplastic Aw49Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP5RPL40SOVF_000530
Find proteins for P27684 (Spinacia oleracea)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-recycling factor, chloroplastic Az191Spinacia oleraceaMutation(s): 0 
Gene Names: RRFFRRHCP
Find proteins for P82231 (Spinacia oleracea)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2, chloroplastic BB215Spinacia oleraceaMutation(s): 0 
Gene Names: rps2
Find proteins for P08242 (Spinacia oleracea)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3, chloroplastic BC217Spinacia oleraceaMutation(s): 0 
Gene Names: rps3
Find proteins for P09595 (Spinacia oleracea)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4, chloroplastic BD200Spinacia oleraceaMutation(s): 0 
Gene Names: rps4
Find proteins for P13788 (Spinacia oleracea)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5, chloroplastic BE158Spinacia oleraceaMutation(s): 0 
Gene Names: rps5SOVF_195380
Find proteins for Q9ST69 (Spinacia oleracea)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6 alpha, chloroplastic BF113Spinacia oleraceaMutation(s): 0 
Gene Names: RPS6SOVF_120630
Find proteins for P82403 (Spinacia oleracea)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7, chloroplastic BG151Spinacia oleraceaMutation(s): 0 
Gene Names: rps7-Arps7-B
Find proteins for P82129 (Spinacia oleracea)
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8, chloroplastic BH134Spinacia oleraceaMutation(s): 0 
Gene Names: rps8
Find proteins for P09597 (Spinacia oleracea)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9, chloroplastic BI141Spinacia oleraceaMutation(s): 0 
Gene Names: PRPS9SOVF_016530
Find proteins for P82278 (Spinacia oleracea)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10 alpha, chloroplastic BJ98Spinacia oleraceaMutation(s): 0 
Gene Names: RPS10SOVF_026730
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11, chloroplastic BK110Spinacia oleraceaMutation(s): 0 
Gene Names: rps11
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12, chloroplastic BL122Spinacia oleraceaMutation(s): 0 
Gene Names: rps12-Arps12-B
Find proteins for P62128 (Spinacia oleracea)
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13, chloroplastic BM111Spinacia oleraceaMutation(s): 0 
Gene Names: RPS13SOVF_121110
Find proteins for P82163 (Spinacia oleracea)
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14, chloroplastic BN99Spinacia oleraceaMutation(s): 0 
Gene Names: rps14
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Entity ID: 48
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30S ribosomal protein S15, chloroplastic BO72Spinacia oleraceaMutation(s): 0 
Gene Names: rps15
Find proteins for Q9M3I4 (Spinacia oleracea)
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16, chloroplastic BP81Spinacia oleraceaMutation(s): 0 
Gene Names: rps16
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Entity ID: 50
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30S ribosomal protein S17, chloroplastic BQ84Spinacia oleraceaMutation(s): 0 
Gene Names: RPS17SOVF_042540
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Entity ID: 51
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30S ribosomal protein S18, chloroplastic BR53Spinacia oleraceaMutation(s): 0 
Gene Names: RPS18
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Entity ID: 52
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30S ribosomal protein S19, chloroplastic BS81Spinacia oleraceaMutation(s): 0 
Gene Names: rps19
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Entity ID: 53
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30S ribosomal protein S20, chloroplastic BT102Spinacia oleraceaMutation(s): 0 
Gene Names: RPS20
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Entity ID: 54
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30S ribosomal protein S21, chloroplastic BU59Spinacia oleraceaMutation(s): 0 
Gene Names: rps21SOVF_070750
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Entity ID: 55
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Ribosome-binding factor PSRP1, chloroplastic BV106Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP1RPS22RPS30SOVF_177810
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S31, chloroplastic BW37Spinacia oleraceaMutation(s): 0 
Gene Names: RPS31PSRP4SOVF_048530
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Entity ID: 57
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bS1c BY170Spinacia oleraceaMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAAA2810Spinacia oleracea
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Entity ID: 2
MoleculeChainsLengthOrganismImage
4.5S ribosomal RNAAB106Spinacia oleracea
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Entity ID: 32
MoleculeChainsLengthOrganismImage
5S ribosomal RNAAx118Spinacia oleracea
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Entity ID: 34
MoleculeChainsLengthOrganismImage
16S ribosomal RNABA1481Spinacia oleracea
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
Ab, Ae
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AA, AB, Af, Aw, Ax, BA, BN
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Foundation for Strategic ResearchSwedenFuture Leaders Grant FFL15:0325
Ragnar Soderberg FoundationSwedenM44/16
Swedish Research CouncilSwedenNT-2016-04107
Swedish Research CouncilSwedenNT-2013-5901

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release