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: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


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: 10.1093/nar/gkw1272

  • 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 eukaryot ...

    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

    Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany.,Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.,Department of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2, chloroplastic
D
272Spinacia oleraceaMutation(s): 0 
Gene Names: rpl2-A, rpl2-B
Find proteins for P06509 (Spinacia oleracea)
Go to UniProtKB:  P06509
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3, chloroplastic
E
305Spinacia oleraceaMutation(s): 0 
Gene Names: RPL3
Find proteins for P82191 (Spinacia oleracea)
Go to Gene View: RPL3
Go to UniProtKB:  P82191
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4, chloroplastic
F
293Spinacia oleraceaMutation(s): 0 
Gene Names: RPL4
Find proteins for O49937 (Spinacia oleracea)
Go to Gene View: RPL4
Go to UniProtKB:  O49937
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5, chloroplastic
G
220Spinacia oleraceaMutation(s): 0 
Gene Names: RPL5 (PrpL5)
Find proteins for P82192 (Spinacia oleracea)
Go to Gene View: RPL5
Go to UniProtKB:  P82192
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6, chloroplastic
H
220Spinacia oleraceaMutation(s): 0 
Gene Names: RPL6
Find proteins for P82193 (Spinacia oleracea)
Go to Gene View: RPL6
Go to UniProtKB:  P82193
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9, chloroplastic
I
196Spinacia oleraceaMutation(s): 0 
Gene Names: RPL9
Find proteins for P82180 (Spinacia oleracea)
Go to Gene View: RPL9
Go to UniProtKB:  P82180
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13, chloroplastic
L
250Spinacia oleraceaMutation(s): 0 
Gene Names: RPL13
Find proteins for P12629 (Spinacia oleracea)
Go to Gene View: RPL13
Go to UniProtKB:  P12629
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14, chloroplastic
M
121Spinacia oleraceaMutation(s): 0 
Gene Names: rpl14
Find proteins for P09596 (Spinacia oleracea)
Go to UniProtKB:  P09596
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15, chloroplastic
N
271Spinacia oleraceaMutation(s): 0 
Gene Names: RPL15
Find proteins for P22798 (Spinacia oleracea)
Go to Gene View: RPL15
Go to UniProtKB:  P22798
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16, chloroplastic
O
135Spinacia oleraceaMutation(s): 0 
Gene Names: rpl16
Find proteins for P17353 (Spinacia oleracea)
Go to UniProtKB:  P17353
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17, chloroplastic
P
126Spinacia oleraceaMutation(s): 0 
Gene Names: RPL17
Find proteins for P82194 (Spinacia oleracea)
Go to Gene View: RPL17
Go to UniProtKB:  P82194
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18, chloroplastic
Q
166Spinacia oleraceaMutation(s): 0 
Gene Names: RPL18 (PRPL18)
Find proteins for P82195 (Spinacia oleracea)
Go to Gene View: RPL18
Go to UniProtKB:  P82195
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19, chloroplastic
R
233Spinacia oleraceaMutation(s): 0 
Gene Names: RPL19 (PRPL19)
Find proteins for P82413 (Spinacia oleracea)
Go to Gene View: RPL19
Go to UniProtKB:  P82413
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20, chloroplastic
S
128Spinacia oleraceaMutation(s): 0 
Gene Names: rpl20
Find proteins for P28803 (Spinacia oleracea)
Go to UniProtKB:  P28803
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21, chloroplastic
T
256Spinacia oleraceaMutation(s): 0 
Gene Names: RPL21
Find proteins for P24613 (Spinacia oleracea)
Go to Gene View: RPL21
Go to UniProtKB:  P24613
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22, chloroplastic
U
199Spinacia oleraceaMutation(s): 0 
Gene Names: rpl22
Find proteins for P09594 (Spinacia oleracea)
Go to UniProtKB:  P09594
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23, chloroplastic
V
198Spinacia oleraceaMutation(s): 0 
Gene Names: RPL23
Find proteins for Q9LWB5 (Spinacia oleracea)
Go to Gene View: RPL23
Go to UniProtKB:  Q9LWB5
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24, chloroplastic
W
191Spinacia oleraceaMutation(s): 0 
Gene Names: RPL24
Find proteins for P27683 (Spinacia oleracea)
Go to Gene View: RPL24
Go to UniProtKB:  P27683
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27, chloroplastic
X
194Spinacia oleraceaMutation(s): 0 
Gene Names: RPL27
Find proteins for P82190 (Spinacia oleracea)
Go to Gene View: RPL27
Go to UniProtKB:  P82190
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28, chloroplastic
Y
148Spinacia oleraceaMutation(s): 0 
Gene Names: RPL28
Find proteins for P82245 (Spinacia oleracea)
Go to Gene View: RPL28
Go to UniProtKB:  P82245
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29, chloroplastic
Z
168Spinacia oleraceaMutation(s): 0 
Gene Names: RPL29
Find proteins for P82248 (Spinacia oleracea)
Go to Gene View: RPL29
Go to UniProtKB:  P82248
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32, chloroplastic
2
57Spinacia 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
3
66Spinacia 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
4
152Spinacia 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
5
159Spinacia 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
6
37Spinacia oleraceaMutation(s): 0 
Gene Names: rpl36
Find proteins for P12230 (Spinacia oleracea)
Go to UniProtKB:  P12230
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Ribosome-recycling factor, chloroplastic
9
271Spinacia oleraceaMutation(s): 0 
Gene Names: RRF (FRRHCP)
Find proteins for P82231 (Spinacia oleracea)
Go to UniProtKB:  P82231
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
PSRP5alpha, chloroplastic
7
142Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP5 (RPL40)
Find proteins for P27684 (Spinacia oleracea)
Go to UniProtKB:  P27684
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
PSRP6, chloroplastic
8
116Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP6
Find proteins for P82411 (Spinacia oleracea)
Go to UniProtKB:  P82411
Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNA, chloroplasticA2811Spinacia oleracea
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNA, chloroplasticB121Spinacia oleracea
Entity ID: 3
MoleculeChainsLengthOrganism
4.8S ribosomal RNA, chloroplasticC103Spinacia oleracea
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

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