5MMI

Structure of the large subunit of the chloroplast ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 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
50S ribosomal protein L32, chloroplastic
1
57Spinacia oleraceaMutation(s): 0 
Gene Names: rpl32
Find proteins for P28804 (Spinacia oleracea)
Go to UniProtKB:  P28804
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33, chloroplastic
2
66Spinacia oleraceaMutation(s): 0 
Gene Names: rpl33
Find proteins for P28805 (Spinacia oleracea)
Go to UniProtKB:  P28805
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34, chloroplastic
3
152Spinacia oleraceaMutation(s): 0 
Gene Names: RPL34
Find proteins for P82244 (Spinacia oleracea)
Go to Gene View: RPL34
Go to UniProtKB:  P82244
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35, chloroplastic
4
159Spinacia oleraceaMutation(s): 0 
Gene Names: RPL35
Find proteins for P23326 (Spinacia oleracea)
Go to Gene View: RPL35
Go to UniProtKB:  P23326
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36, chloroplastic
5
37Spinacia oleraceaMutation(s): 0 
Gene Names: rpl36
Find proteins for P12230 (Spinacia oleracea)
Go to UniProtKB:  P12230
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein cL37, PSRP5
6
142Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP5 (RPL40)
Find proteins for P27684 (Spinacia oleracea)
Go to UniProtKB:  P27684
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein 6, chloroplastic
7
116Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP6
Find proteins for P82411 (Spinacia oleracea)
Go to UniProtKB:  P82411
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2, chloroplastic
C
272Spinacia oleraceaMutation(s): 0 
Gene Names: rpl2-A, rpl2-B
Find proteins for P06509 (Spinacia oleracea)
Go to UniProtKB:  P06509
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uL3c
D
305Spinacia oleraceaMutation(s): 0 
Gene Names: RPL3
Find proteins for P82191 (Spinacia oleracea)
Go to Gene View: RPL3
Go to UniProtKB:  P82191
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uL4c
E
293Spinacia oleraceaMutation(s): 0 
Gene Names: RPL4
Find proteins for O49937 (Spinacia oleracea)
Go to Gene View: RPL4
Go to UniProtKB:  O49937
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uL5c
F
258Spinacia oleraceaMutation(s): 0 
Gene Names: RPL5 (PrpL5)
Find proteins for P82192 (Spinacia oleracea)
Go to Gene View: RPL5
Go to UniProtKB:  P82192
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uL6c
G
220Spinacia oleraceaMutation(s): 0 
Gene Names: RPL6
Find proteins for P82193 (Spinacia oleracea)
Go to Gene View: RPL6
Go to UniProtKB:  P82193
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein bL9c
H
196Spinacia oleraceaMutation(s): 0 
Gene Names: RPL9
Find proteins for P82180 (Spinacia oleracea)
Go to Gene View: RPL9
Go to UniProtKB:  P82180
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uL10c
I
232Spinacia oleraceaMutation(s): 0 
Gene Names: RPL10
Find proteins for P82139 (Spinacia oleracea)
Go to Gene View: RPL10
Go to UniProtKB:  P82139
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11, chloroplastic
J
224Spinacia oleraceaMutation(s): 0 
Gene Names: rpl11
Find proteins for P31164 (Spinacia oleracea)
Go to UniProtKB:  P31164
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13, chloroplastic
K
250Spinacia oleraceaMutation(s): 0 
Gene Names: RPL13
Find proteins for P12629 (Spinacia oleracea)
Go to Gene View: RPL13
Go to UniProtKB:  P12629
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14, chloroplastic
L
121Spinacia oleraceaMutation(s): 0 
Gene Names: rpl14
Find proteins for P09596 (Spinacia oleracea)
Go to UniProtKB:  P09596
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uL15c
M
271Spinacia oleraceaMutation(s): 0 
Gene Names: RPL15
Find proteins for P22798 (Spinacia oleracea)
Go to Gene View: RPL15
Go to UniProtKB:  P22798
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16, chloroplastic
N
135Spinacia oleraceaMutation(s): 0 
Gene Names: rpl16
Find proteins for P17353 (Spinacia oleracea)
Go to UniProtKB:  P17353
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein bL17c
O
126Spinacia oleraceaMutation(s): 0 
Gene Names: RPL17
Find proteins for P82194 (Spinacia oleracea)
Go to Gene View: RPL17
Go to UniProtKB:  P82194
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uL18c
P
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: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19, chloroplastic
Q
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: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20, chloroplastic
R
128Spinacia oleraceaMutation(s): 0 
Gene Names: rpl20
Find proteins for P28803 (Spinacia oleracea)
Go to UniProtKB:  P28803
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21, chloroplastic
S
256Spinacia oleraceaMutation(s): 0 
Gene Names: RPL21
Find proteins for P24613 (Spinacia oleracea)
Go to Gene View: RPL21
Go to UniProtKB:  P24613
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22, chloroplastic
T
199Spinacia oleraceaMutation(s): 0 
Gene Names: rpl22
Find proteins for P09594 (Spinacia oleracea)
Go to UniProtKB:  P09594
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23, chloroplastic
U
198Spinacia oleraceaMutation(s): 0 
Gene Names: RPL23
Find proteins for Q9LWB5 (Spinacia oleracea)
Go to Gene View: RPL23
Go to UniProtKB:  Q9LWB5
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uL24c
V
192Spinacia oleraceaMutation(s): 0 
Gene Names: RPL24
Find proteins for P27683 (Spinacia oleracea)
Go to Gene View: RPL24
Go to UniProtKB:  P27683
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein bL27c
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: 33
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein bL28c
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: 34
MoleculeChainsSequence LengthOrganismDetails
plastid ribosomal protein uL29c
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: 9
MoleculeChainsLengthOrganism
23S ribosomal RNAA2810Spinacia oleracea
Entity ID: 10
MoleculeChainsLengthOrganism
5S ribosomal RNAB121Spinacia oleracea
Entity ID: 31
MoleculeChainsLengthOrganism
4.5S ribosomal RNAW106Spinacia oleracea
Entity ID: 35
MoleculeChainsLengthOrganism
E-site tRNAz2Spinacia oleracea
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
2, 5
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
4, 6, 7, A, B, C, D, E, H, M, N, P, R, T, U, V, W, X, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 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