5MMJ

Structure of the small subunit of the chloroplast ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.5 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: https://doi.org/10.15252/embj.201695959
  • Primary Citation of Related Structures:  
    5MMI, 5MMJ, 5MMM

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31A [auth 0]130Spinacia oleraceaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein bS1cB [auth 8]174Spinacia oleraceaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2, chloroplasticD [auth b]236Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3, chloroplasticE [auth c]218Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4, chloroplasticF [auth d]201Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5, chloroplasticG [auth e]308Spinacia oleraceaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein bS6cH [auth f]211Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7, chloroplasticI [auth g]155Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8, chloroplasticJ [auth h]134Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uS9cK [auth i]208Spinacia oleraceaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uS10cL [auth j]195Spinacia oleraceaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11, chloroplasticM [auth k]138Spinacia oleraceaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12, chloroplasticN [auth l]123Spinacia oleraceaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uS13cO [auth m]172Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14, chloroplasticP [auth n]100Spinacia oleraceaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15, chloroplasticQ [auth o]90Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16, chloroplasticR [auth p]88Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein uS17cS [auth q]165Spinacia oleraceaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18, chloroplasticT [auth r]101Spinacia oleraceaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19 alpha, chloroplasticU [auth s]92Spinacia oleraceaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein bS20cV [auth t]183Spinacia oleraceaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
plastid ribosomal protein bS21cW [auth u]180Spinacia oleraceaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein 2, chloroplasticX [auth v]260Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein 3, chloroplasticY [auth w]179Spinacia oleraceaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S31, chloroplasticZ [auth x]101Spinacia oleraceaMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-binding factor PSRP1, chloroplasticAA [auth y]302Spinacia oleraceaMutation(s): 0 
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Entity ID: 3
MoleculeChains LengthOrganismImage
16S ribosomal RNAC [auth a]1,491Spinacia oleracea
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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AB [auth a]
AC [auth a]
AD [auth a]
AE [auth a]
AF [auth a]
AB [auth a],
AC [auth a],
AD [auth a],
AE [auth a],
AF [auth a],
AG [auth a],
AH [auth a],
BA [auth a],
BB [auth a],
BC [auth a],
BD [auth a],
BE [auth a],
BF [auth a],
BG [auth a],
BH [auth k],
CA [auth a],
CB [auth a],
CC [auth a],
CD [auth a],
CE [auth a],
CF [auth a],
CG [auth a],
CH [auth l],
DA [auth a],
DB [auth a],
DC [auth a],
DD [auth a],
DE [auth a],
DF [auth a],
DG [auth a],
DH [auth x],
EA [auth a],
EB [auth a],
EC [auth a],
ED [auth a],
EE [auth a],
EF [auth a],
EG [auth a],
FA [auth a],
FB [auth a],
FC [auth a],
FD [auth a],
FE [auth a],
FF [auth a],
FG [auth a],
GA [auth a],
GB [auth a],
GC [auth a],
GD [auth a],
GE [auth a],
GF [auth a],
GG [auth a],
HA [auth a],
HB [auth a],
HC [auth a],
HD [auth a],
HE [auth a],
HF [auth a],
HG [auth a],
IA [auth a],
IB [auth a],
IC [auth a],
ID [auth a],
IE [auth a],
IF [auth a],
IG [auth a],
JA [auth a],
JB [auth a],
JC [auth a],
JD [auth a],
JE [auth a],
JF [auth a],
JG [auth a],
KA [auth a],
KB [auth a],
KC [auth a],
KD [auth a],
KE [auth a],
KF [auth a],
KG [auth a],
LA [auth a],
LB [auth a],
LC [auth a],
LD [auth a],
LE [auth a],
LF [auth a],
LG [auth a],
MA [auth a],
MB [auth a],
MC [auth a],
MD [auth a],
ME [auth a],
MF [auth a],
MG [auth a],
NA [auth a],
NB [auth a],
NC [auth a],
ND [auth a],
NE [auth a],
NF [auth a],
NG [auth a],
OA [auth a],
OB [auth a],
OC [auth a],
OD [auth a],
OE [auth a],
OF [auth a],
OG [auth a],
PA [auth a],
PB [auth a],
PC [auth a],
PD [auth a],
PE [auth a],
PF [auth a],
PG [auth a],
QA [auth a],
QB [auth a],
QC [auth a],
QD [auth a],
QE [auth a],
QF [auth a],
QG [auth a],
RA [auth a],
RB [auth a],
RC [auth a],
RD [auth a],
RE [auth a],
RF [auth a],
RG [auth a],
SA [auth a],
SB [auth a],
SC [auth a],
SD [auth a],
SE [auth a],
SF [auth a],
SG [auth a],
TA [auth a],
TB [auth a],
TC [auth a],
TD [auth a],
TE [auth a],
TF [auth a],
TG [auth a],
UA [auth a],
UB [auth a],
UC [auth a],
UD [auth a],
UE [auth a],
UF [auth a],
UG [auth a],
VA [auth a],
VB [auth a],
VC [auth a],
VD [auth a],
VE [auth a],
VF [auth a],
VG [auth a],
WA [auth a],
WB [auth a],
WC [auth a],
WD [auth a],
WE [auth a],
WF [auth a],
WG [auth a],
XA [auth a],
XB [auth a],
XC [auth a],
XD [auth a],
XE [auth a],
XF [auth a],
XG [auth a],
YA [auth a],
YB [auth a],
YC [auth a],
YD [auth a],
YE [auth a],
YF [auth a],
YG [auth a],
ZA [auth a],
ZB [auth a],
ZC [auth a],
ZD [auth a],
ZE [auth a],
ZF [auth a],
ZG [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIX1.11.1

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.3: 2018-10-17
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-12-11
    Changes: Other
  • Version 1.5: 2024-05-15
    Changes: Data collection, Database references, Derived calculations, Refinement description