5X8R

Structure of the 30S small subunit of chloroplast ribosome from spinach


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 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

Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation

Ahmed, T.Shi, J.Bhushan, S.

(2017) Nucleic Acids Res. 45: 8581-8595

  • DOI: 10.1093/nar/gkx499
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggest ...

    Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggested to play important regulatory roles in translation. However, their exact locations on the chloroplast ribosome remain elusive due to lack of a high-resolution structure, hindering our progress to understand their possible roles. Here we present a cryo-EM structure of the 70S chloroplast ribosome from spinach resolved to 3.4 Å and focus our discussion mainly on the architecture of the 30S small subunit (SSU) which is resolved to 3.7 Å. cS22 localizes at the SSU foot where it seems to compensate for the deletions in 16S rRNA. The mRNA exit site is highly remodeled due to the presence of cS23 suggesting an alternative mode of translation initiation. bTHXc is positioned at the SSU head and appears to stabilize the intersubunit bridge B1b during thermal fluctuations. The translation factor plastid pY binds to the SSU on the intersubunit side and interacts with the conserved nucleotide bases involved in decoding. Most of the intersubunit bridges are conserved compared to the bacteria, except for a new bridge involving uL2c and bS6c.


    Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, 637551, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
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: 2
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: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5, chloroplastic
e
253Spinacia oleraceaMutation(s): 0 
Gene Names: rps5
Find proteins for Q9ST69 (Spinacia oleracea)
Go to UniProtKB:  Q9ST69
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6 alpha, chloroplastic
f
146Spinacia oleraceaMutation(s): 0 
Gene Names: RPS6
Find proteins for P82403 (Spinacia oleracea)
Go to Gene View: RPS6
Go to UniProtKB:  P82403
Entity ID: 5
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: 6
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: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9, chloroplastic
i
157Spinacia oleraceaMutation(s): 0 
Gene Names: PRPS9
Find proteins for P82278 (Spinacia oleracea)
Go to UniProtKB:  P82278
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
protein S10
j
122Spinacia oleraceaMutation(s): 0 
Gene Names: RPS10
Find proteins for P82162 (Spinacia oleracea)
Go to Gene View: RPS10
Go to UniProtKB:  P82162
Entity ID: 9
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: 10
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: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13, chloroplastic
m
126Oryza sativa subsp. indicaMutation(s): 0 
Find proteins for B8AQA7 (Oryza sativa subsp. indica)
Go to UniProtKB:  B8AQA7
Entity ID: 12
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: 13
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: 14
MoleculeChainsSequence LengthOrganismDetails
protein S17
q
108Spinacia oleraceaMutation(s): 0 
Gene Names: RPS17
Find proteins for P82137 (Spinacia oleracea)
Go to Gene View: RPS17
Go to UniProtKB:  P82137
Entity ID: 15
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: 16
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: 17
MoleculeChainsSequence LengthOrganismDetails
protein S20
t
108Spinacia oleraceaMutation(s): 0 
Gene Names: RPS20
Find proteins for P82130 (Spinacia oleracea)
Go to Gene View: RPS20
Go to UniProtKB:  P82130
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
protein S21
u
137Spinacia oleraceaMutation(s): 0 
Gene Names: rps21
Find proteins for P82024 (Spinacia oleracea)
Go to UniProtKB:  P82024
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
protein plastid pY
y
236Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP1 (RPS22, RPS30)
Find proteins for P19954 (Spinacia oleracea)
Go to UniProtKB:  P19954
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
protein cS23
w
121Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP3
Find proteins for P82412 (Spinacia oleracea)
Go to UniProtKB:  P82412
Entity ID: 22
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: 23
MoleculeChainsSequence LengthOrganismDetails
protein cS22
v
198Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP2
Find proteins for P82277 (Spinacia oleracea)
Go to UniProtKB:  P82277
Entity ID: 24
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: 25
MoleculeChainsSequence LengthOrganismDetails
protein bTHXc
x
47Spinacia oleraceaMutation(s): 0 
Gene Names: RPS31 (PSRP4)
Find proteins for P47910 (Spinacia oleracea)
Go to UniProtKB:  P47910
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S1, chloroplastic
8
370Spinacia oleraceaMutation(s): 0 
Gene Names: RPS1
Find proteins for P29344 (Spinacia oleracea)
Go to UniProtKB:  P29344
Entity ID: 20
MoleculeChainsLengthOrganism
16S rRNAa1491Spinacia oleracea
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 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
MOESingaporeAcRF Tier 1, 2014-T1-001-019 (RG32/14)

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-06-14
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Database references
  • Version 1.3: 2018-06-06
    Type: Data collection