5MMJ

Structure of the small subunit of the chloroplast ribosome


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 1.3 of the entry. See complete history

Literature

The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.

Bieri, P.Leibundgut, M.Saurer, M.Boehringer, D.Ban, N.

(2017) EMBO J. 36: 475-486

  • DOI: 10.15252/embj.201695959
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machin ...

    Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
0
130Spinacia oleraceaMutation(s): 0 
Gene Names: RPL31
Find proteins for P82249 (Spinacia oleracea)
Go to Gene View: RPL31
Go to UniProtKB:  P82249
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein bS1c
8
174N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2, chloroplastic
b
236Spinacia oleraceaMutation(s): 0 
Gene Names: rps2
Find proteins for P08242 (Spinacia oleracea)
Go to UniProtKB:  P08242
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3, chloroplastic
c
218Spinacia oleraceaMutation(s): 0 
Gene Names: rps3
Find proteins for P09595 (Spinacia oleracea)
Go to UniProtKB:  P09595
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4, chloroplastic
d
201Spinacia oleraceaMutation(s): 0 
Gene Names: rps4
Find proteins for P13788 (Spinacia oleracea)
Go to UniProtKB:  P13788
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5, chloroplastic
e
308Spinacia oleraceaMutation(s): 0 
Gene Names: rps5
Find proteins for Q9ST69 (Spinacia oleracea)
Go to UniProtKB:  Q9ST69
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein bS6c
f
211Spinacia oleraceaMutation(s): 0 
Gene Names: RPS6
Find proteins for P82403 (Spinacia oleracea)
Go to Gene View: RPS6
Go to UniProtKB:  P82403
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7, chloroplastic
g
155Spinacia oleraceaMutation(s): 0 
Gene Names: rps7-A, rps7-B
Find proteins for P82129 (Spinacia oleracea)
Go to UniProtKB:  P82129
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8, chloroplastic
h
134Spinacia oleraceaMutation(s): 0 
Gene Names: rps8
Find proteins for P09597 (Spinacia oleracea)
Go to UniProtKB:  P09597
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uS9c
i
208Spinacia oleraceaMutation(s): 0 
Gene Names: PRPS9
Find proteins for P82278 (Spinacia oleracea)
Go to UniProtKB:  P82278
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uS10c
j
195Spinacia oleraceaMutation(s): 0 
Gene Names: RPS10
Find proteins for P82162 (Spinacia oleracea)
Go to Gene View: RPS10
Go to UniProtKB:  P82162
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11, chloroplastic
k
138Spinacia oleraceaMutation(s): 0 
Gene Names: rps11
Find proteins for P06506 (Spinacia oleracea)
Go to UniProtKB:  P06506
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12, chloroplastic
l
123Spinacia oleraceaMutation(s): 0 
Gene Names: rps12-A, rps12-B
Find proteins for P62128 (Spinacia oleracea)
Go to UniProtKB:  P62128
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uS13c
m
172Spinacia oleraceaMutation(s): 0 
Gene Names: RPS13
Find proteins for P82163 (Spinacia oleracea)
Go to Gene View: RPS13
Go to UniProtKB:  P82163
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14, chloroplastic
n
100Spinacia oleraceaMutation(s): 0 
Gene Names: rps14
Find proteins for P06507 (Spinacia oleracea)
Go to UniProtKB:  P06507
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15, chloroplastic
o
90Spinacia oleraceaMutation(s): 0 
Gene Names: rps15
Find proteins for Q9M3I4 (Spinacia oleracea)
Go to UniProtKB:  Q9M3I4
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16, chloroplastic
p
88Spinacia oleraceaMutation(s): 0 
Gene Names: rps16
Find proteins for P28807 (Spinacia oleracea)
Go to UniProtKB:  P28807
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uS17c
q
165Spinacia oleraceaMutation(s): 0 
Gene Names: RPS17
Find proteins for P82137 (Spinacia oleracea)
Go to Gene View: RPS17
Go to UniProtKB:  P82137
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18, chloroplastic
r
101Spinacia oleraceaMutation(s): 0 
Gene Names: RPS18
Find proteins for Q9M3K7 (Spinacia oleracea)
Go to Gene View: RPS18
Go to UniProtKB:  Q9M3K7
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19 alpha, chloroplastic
s
92Spinacia oleraceaMutation(s): 0 
Gene Names: rps19
Find proteins for P06508 (Spinacia oleracea)
Go to UniProtKB:  P06508
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein bS20c
t
183N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein bS21c
u
180Spinacia oleraceaMutation(s): 0 
Gene Names: rps21
Find proteins for P82024 (Spinacia oleracea)
Go to UniProtKB:  P82024
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein 2, chloroplastic
v
260Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP2
Find proteins for P82277 (Spinacia oleracea)
Go to UniProtKB:  P82277
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein 3, chloroplastic
w
179Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP3
Find proteins for P82412 (Spinacia oleracea)
Go to UniProtKB:  P82412
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S31, chloroplastic
x
101Spinacia oleraceaMutation(s): 0 
Gene Names: RPS31 (PSRP4)
Find proteins for P47910 (Spinacia oleracea)
Go to UniProtKB:  P47910
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosome-binding factor PSRP1, chloroplastic
y
302Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP1 (RPS22, RPS30)
Find proteins for P19954 (Spinacia oleracea)
Go to UniProtKB:  P19954
Entity ID: 3
MoleculeChainsLengthOrganism
16S ribosomal RNAa1491Spinacia oleracea
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
a, k, l, x
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
8
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-03-01
    Type: Database references
  • Version 1.2: 2017-08-02
    Type: Data collection, Derived calculations
  • Version 1.3: 2018-10-17
    Type: Data collection, Other, Refinement description