6ERI

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 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

  • 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 ...

    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.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden. amunts@scilifelab.se.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2, chloroplastic
AC
246Spinacia oleraceaMutation(s): 0 
Gene Names: rpl2-A, rpl2-B
Find proteins for P06509 (Spinacia oleracea)
Go to UniProtKB:  P06509
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3, chloroplastic
AD
221Spinacia oleraceaMutation(s): 0 
Gene Names: RPL3
Find proteins for P82191 (Spinacia oleracea)
Go to Gene View: RPL3
Go to UniProtKB:  P82191
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4, chloroplastic
AE
212Spinacia oleraceaMutation(s): 0 
Gene Names: RPL4
Find proteins for O49937 (Spinacia oleracea)
Go to Gene View: RPL4
Go to UniProtKB:  O49937
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5, chloroplastic
AF
207Spinacia oleraceaMutation(s): 0 
Gene Names: RPL5 (PrpL5)
Find proteins for P82192 (Spinacia oleracea)
Go to Gene View: RPL5
Go to UniProtKB:  P82192
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6, chloroplastic
AG
172Spinacia oleraceaMutation(s): 0 
Gene Names: RPL6
Find proteins for P82193 (Spinacia oleracea)
Go to Gene View: RPL6
Go to UniProtKB:  P82193
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9, chloroplastic
AH
46Spinacia oleraceaMutation(s): 0 
Gene Names: RPL9
Find proteins for P82180 (Spinacia oleracea)
Go to Gene View: RPL9
Go to UniProtKB:  P82180
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13, chloroplastic
AJ
200Spinacia oleraceaMutation(s): 0 
Gene Names: RPL13
Find proteins for P12629 (Spinacia oleracea)
Go to Gene View: RPL13
Go to UniProtKB:  P12629
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14, chloroplastic
AK
121Spinacia oleraceaMutation(s): 0 
Gene Names: rpl14
Find proteins for P09596 (Spinacia oleracea)
Go to UniProtKB:  P09596
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15, chloroplastic
AL
184Spinacia oleraceaMutation(s): 0 
Gene Names: RPL15
Find proteins for P22798 (Spinacia oleracea)
Go to Gene View: RPL15
Go to UniProtKB:  P22798
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16, chloroplastic
AM
134Spinacia oleraceaMutation(s): 0 
Gene Names: rpl16
Find proteins for P17353 (Spinacia oleracea)
Go to UniProtKB:  P17353
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17, chloroplastic
AN
116Spinacia oleraceaMutation(s): 0 
Gene Names: RPL17
Find proteins for P82194 (Spinacia oleracea)
Go to Gene View: RPL17
Go to UniProtKB:  P82194
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18, chloroplastic
AO
121Spinacia oleraceaMutation(s): 0 
Gene Names: RPL18 (PRPL18)
Find proteins for P82195 (Spinacia oleracea)
Go to Gene View: RPL18
Go to UniProtKB:  P82195
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19, chloroplastic
AP
118Spinacia oleraceaMutation(s): 0 
Gene Names: RPL19 (PRPL19)
Find proteins for P82413 (Spinacia oleracea)
Go to Gene View: RPL19
Go to UniProtKB:  P82413
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20, chloroplastic
AQ
115Spinacia oleraceaMutation(s): 0 
Gene Names: rpl20
Find proteins for P28803 (Spinacia oleracea)
Go to UniProtKB:  P28803
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21, chloroplastic
AR
165Spinacia oleraceaMutation(s): 0 
Gene Names: RPL21
Find proteins for P24613 (Spinacia oleracea)
Go to Gene View: RPL21
Go to UniProtKB:  P24613
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22, chloroplastic
AS
171Spinacia oleraceaMutation(s): 0 
Gene Names: rpl22
Find proteins for P09594 (Spinacia oleracea)
Go to UniProtKB:  P09594
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23, chloroplastic
AT
92Spinacia oleraceaMutation(s): 0 
Gene Names: RPL23
Find proteins for Q9LWB5 (Spinacia oleracea)
Go to Gene View: RPL23
Go to UniProtKB:  Q9LWB5
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24, chloroplastic
AU
127Spinacia oleraceaMutation(s): 0 
Gene Names: RPL24
Find proteins for P27683 (Spinacia oleracea)
Go to Gene View: RPL24
Go to UniProtKB:  P27683
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27, chloroplastic
AW
114Spinacia oleraceaMutation(s): 0 
Gene Names: RPL27
Find proteins for P82190 (Spinacia oleracea)
Go to Gene View: RPL27
Go to UniProtKB:  P82190
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28, chloroplastic
AX
76Spinacia oleraceaMutation(s): 0 
Gene Names: RPL28
Find proteins for P82245 (Spinacia oleracea)
Go to Gene View: RPL28
Go to UniProtKB:  P82245
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29, chloroplastic
AY
99Spinacia oleraceaMutation(s): 0 
Gene Names: RPL29
Find proteins for P82248 (Spinacia oleracea)
Go to Gene View: RPL29
Go to UniProtKB:  P82248
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31, chloroplastic
AZ
66Spinacia oleraceaMutation(s): 0 
Gene Names: RPL31
Find proteins for P82249 (Spinacia oleracea)
Go to Gene View: RPL31
Go to UniProtKB:  P82249
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32, chloroplastic
Aa
48Spinacia oleraceaMutation(s): 0 
Gene Names: rpl32
Find proteins for P28804 (Spinacia oleracea)
Go to UniProtKB:  P28804
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33, chloroplastic
Ab
60Spinacia oleraceaMutation(s): 0 
Gene Names: rpl33
Find proteins for P28805 (Spinacia oleracea)
Go to UniProtKB:  P28805
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34, chloroplastic
Ac
61Spinacia oleraceaMutation(s): 0 
Gene Names: RPL34
Find proteins for P82244 (Spinacia oleracea)
Go to Gene View: RPL34
Go to UniProtKB:  P82244
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35, chloroplastic
Ad
72Spinacia oleraceaMutation(s): 0 
Gene Names: RPL35
Find proteins for P23326 (Spinacia oleracea)
Go to Gene View: RPL35
Go to UniProtKB:  P23326
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36, chloroplastic
Ae
37Spinacia oleraceaMutation(s): 0 
Gene Names: rpl36
Find proteins for P12230 (Spinacia oleracea)
Go to UniProtKB:  P12230
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein 6, chloroplastic
Af
47Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP6
Find proteins for P82411 (Spinacia oleracea)
Go to UniProtKB:  P82411
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein 5 alpha, chloroplastic
Aw
49Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP5 (RPL40)
Find proteins for P27684 (Spinacia oleracea)
Go to UniProtKB:  P27684
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ribosome-recycling factor, chloroplastic
Az
191Spinacia oleraceaMutation(s): 0 
Gene Names: RRF (FRRHCP)
Find proteins for P82231 (Spinacia oleracea)
Go to UniProtKB:  P82231
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2, chloroplastic
BB
215Spinacia oleraceaMutation(s): 0 
Gene Names: rps2
Find proteins for P08242 (Spinacia oleracea)
Go to UniProtKB:  P08242
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3, chloroplastic
BC
217Spinacia oleraceaMutation(s): 0 
Gene Names: rps3
Find proteins for P09595 (Spinacia oleracea)
Go to UniProtKB:  P09595
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4, chloroplastic
BD
200Spinacia oleraceaMutation(s): 0 
Gene Names: rps4
Find proteins for P13788 (Spinacia oleracea)
Go to UniProtKB:  P13788
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5, chloroplastic
BE
158Spinacia oleraceaMutation(s): 0 
Gene Names: rps5
Find proteins for Q9ST69 (Spinacia oleracea)
Go to UniProtKB:  Q9ST69
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6 alpha, chloroplastic
BF
113Spinacia oleraceaMutation(s): 0 
Gene Names: RPS6
Find proteins for P82403 (Spinacia oleracea)
Go to Gene View: RPS6
Go to UniProtKB:  P82403
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7, chloroplastic
BG
151Spinacia oleraceaMutation(s): 0 
Gene Names: rps7-A, rps7-B
Find proteins for P82129 (Spinacia oleracea)
Go to UniProtKB:  P82129
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8, chloroplastic
BH
134Spinacia oleraceaMutation(s): 0 
Gene Names: rps8
Find proteins for P09597 (Spinacia oleracea)
Go to UniProtKB:  P09597
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9, chloroplastic
BI
141Spinacia oleraceaMutation(s): 0 
Gene Names: PRPS9
Find proteins for P82278 (Spinacia oleracea)
Go to UniProtKB:  P82278
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10 alpha, chloroplastic
BJ
98Spinacia oleraceaMutation(s): 0 
Gene Names: RPS10
Find proteins for P82162 (Spinacia oleracea)
Go to Gene View: RPS10
Go to UniProtKB:  P82162
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11, chloroplastic
BK
110Spinacia oleraceaMutation(s): 0 
Gene Names: rps11
Find proteins for P06506 (Spinacia oleracea)
Go to UniProtKB:  P06506
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12, chloroplastic
BL
122Spinacia oleraceaMutation(s): 0 
Gene Names: rps12-A, rps12-B
Find proteins for P62128 (Spinacia oleracea)
Go to UniProtKB:  P62128
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13, chloroplastic
BM
111Spinacia oleraceaMutation(s): 0 
Gene Names: RPS13
Find proteins for P82163 (Spinacia oleracea)
Go to Gene View: RPS13
Go to UniProtKB:  P82163
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14, chloroplastic
BN
99Spinacia oleraceaMutation(s): 0 
Gene Names: rps14
Find proteins for P06507 (Spinacia oleracea)
Go to UniProtKB:  P06507
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15, chloroplastic
BO
72Spinacia oleraceaMutation(s): 0 
Gene Names: rps15
Find proteins for Q9M3I4 (Spinacia oleracea)
Go to UniProtKB:  Q9M3I4
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16, chloroplastic
BP
81Spinacia oleraceaMutation(s): 0 
Gene Names: rps16
Find proteins for P28807 (Spinacia oleracea)
Go to UniProtKB:  P28807
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17, chloroplastic
BQ
84Spinacia oleraceaMutation(s): 0 
Gene Names: RPS17
Find proteins for P82137 (Spinacia oleracea)
Go to Gene View: RPS17
Go to UniProtKB:  P82137
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18, chloroplastic
BR
53Spinacia oleraceaMutation(s): 0 
Gene Names: RPS18
Find proteins for Q9M3K7 (Spinacia oleracea)
Go to Gene View: RPS18
Go to UniProtKB:  Q9M3K7
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19, chloroplastic
BS
81Spinacia oleraceaMutation(s): 0 
Gene Names: rps19
Find proteins for P06508 (Spinacia oleracea)
Go to UniProtKB:  P06508
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20, chloroplastic
BT
102Spinacia oleraceaMutation(s): 0 
Gene Names: RPS20
Find proteins for P82130 (Spinacia oleracea)
Go to Gene View: RPS20
Go to UniProtKB:  P82130
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21, chloroplastic
BU
59Spinacia oleraceaMutation(s): 0 
Gene Names: rps21
Find proteins for P82024 (Spinacia oleracea)
Go to UniProtKB:  P82024
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Ribosome-binding factor PSRP1, chloroplastic
BV
106Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP1 (RPS22, RPS30)
Find proteins for P19954 (Spinacia oleracea)
Go to UniProtKB:  P19954
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S31, chloroplastic
BW
37Spinacia oleraceaMutation(s): 0 
Gene Names: RPS31 (PSRP4)
Find proteins for P47910 (Spinacia oleracea)
Go to UniProtKB:  P47910
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
bS1c
BY
170N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNAAA2810Spinacia oleracea
Entity ID: 2
MoleculeChainsLengthOrganism
4.5S ribosomal RNAAB106Spinacia oleracea
Entity ID: 32
MoleculeChainsLengthOrganism
5S ribosomal RNAAx118Spinacia oleracea
Entity ID: 34
MoleculeChainsLengthOrganism
16S ribosomal RNABA1481Spinacia oleracea
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
AA, AB, Af, Aw, Ax, BA, BN
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
BY
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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