5H1S

Structure of the large subunit of the chloro-ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM structure of the large subunit of the spinach chloroplast ribosome.

Ahmed, T.Yin, Z.Bhushan, S.

(2016) Sci Rep 6: 35793-35793

  • DOI: 10.1038/srep35793

  • PubMed Abstract: 
  • Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ribosome but certain differences are evident. The ch ...

    Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ribosome but certain differences are evident. The chloro-ribosome proteins are generally larger because of the presence of chloroplast-specific extensions in their N- and C-termini. The chloro-ribosome harbours six plastid-specific ribosomal proteins (PSRPs); four in the small subunit and two in the large subunit. Deletions and insertions occur throughout the rRNA sequence of the chloro-ribosome (except for the conserved peptidyl transferase center region) but the overall length of the rRNAs do not change significantly, compared to the E. coli. Although, recent advancements in cryo-electron microscopy (cryo-EM) have provided detailed high-resolution structures of ribosomes from many different sources, a high-resolution structure of the chloro-ribosome is still lacking. Here, we present a cryo-EM structure of the large subunit of the chloro-ribosome from spinach (Spinacia oleracea) at an average resolution of 3.5 Å. High-resolution map enabled us to localize and model chloro-ribosome proteins, chloroplast-specific protein extensions, two PSRPs (PSRP5 and 6) and three rRNA molecules present in the chloro-ribosome. Although comparable to E. coli, the polypeptide tunnel and the tunnel exit site show chloroplast-specific features.


    Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13, chloroplastic
L
191Spinacia oleraceaMutation(s): 0 
Gene Names: RPL13
Find proteins for P12629 (Spinacia oleracea)
Go to Gene View: RPL13
Go to UniProtKB:  P12629
Entity ID: 5
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: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
N
192Spinacia oleraceaMutation(s): 0 
Gene Names: RPL15
Find proteins for P22798 (Spinacia oleracea)
Go to Gene View: RPL15
Go to UniProtKB:  P22798
Entity ID: 7
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: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
P
116Spinacia oleraceaMutation(s): 0 
Gene Names: RPL17
Find proteins for P82194 (Spinacia oleracea)
Go to Gene View: RPL17
Go to UniProtKB:  P82194
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
Q
123Spinacia oleraceaMutation(s): 0 
Gene Names: RPL18 (PRPL18)
Find proteins for P82195 (Spinacia oleracea)
Go to Gene View: RPL18
Go to UniProtKB:  P82195
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19, chloroplastic
R
156Spinacia oleraceaMutation(s): 0 
Gene Names: RPL19 (PRPL19)
Find proteins for P82413 (Spinacia oleracea)
Go to Gene View: RPL19
Go to UniProtKB:  P82413
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20, chloroplastic
S
127Spinacia oleraceaMutation(s): 0 
Gene Names: rpl20
Find proteins for P28803 (Spinacia oleracea)
Go to UniProtKB:  P28803
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21, chloroplastic
T
201Spinacia oleraceaMutation(s): 0 
Gene Names: RPL21
Find proteins for P24613 (Spinacia oleracea)
Go to Gene View: RPL21
Go to UniProtKB:  P24613
Entity ID: 13
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: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23, chloroplastic
V
122Spinacia oleraceaMutation(s): 0 
Gene Names: RPL23
Find proteins for Q9LWB5 (Spinacia oleracea)
Go to Gene View: RPL23
Go to UniProtKB:  Q9LWB5
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24, chloroplastic
W
145Spinacia oleraceaMutation(s): 0 
Gene Names: RPL24
Find proteins for P27683 (Spinacia oleracea)
Go to Gene View: RPL24
Go to UniProtKB:  P27683
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
X
137Spinacia oleraceaMutation(s): 0 
Gene Names: RPL27
Find proteins for P82190 (Spinacia oleracea)
Go to Gene View: RPL27
Go to UniProtKB:  P82190
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
Y
77Spinacia oleraceaMutation(s): 0 
Gene Names: RPL28
Find proteins for P82245 (Spinacia oleracea)
Go to Gene View: RPL28
Go to UniProtKB:  P82245
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Z
109Spinacia oleraceaMutation(s): 0 
Gene Names: RPL29
Find proteins for P82248 (Spinacia oleracea)
Go to Gene View: RPL29
Go to UniProtKB:  P82248
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2, chloroplastic
E
271Spinacia oleraceaMutation(s): 0 
Gene Names: rpl2-A, rpl2-B
Find proteins for P06509 (Spinacia oleracea)
Go to UniProtKB:  P06509
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32, chloroplastic
b
56Spinacia oleraceaMutation(s): 0 
Gene Names: rpl32
Find proteins for P28804 (Spinacia oleracea)
Go to UniProtKB:  P28804
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33, chloroplastic
c
65Spinacia oleraceaMutation(s): 0 
Gene Names: rpl33
Find proteins for P28805 (Spinacia oleracea)
Go to UniProtKB:  P28805
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34, chloroplastic
d
60Spinacia oleraceaMutation(s): 0 
Gene Names: RPL34
Find proteins for P82244 (Spinacia oleracea)
Go to Gene View: RPL34
Go to UniProtKB:  P82244
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35, chloroplastic
e
73Spinacia oleraceaMutation(s): 0 
Gene Names: RPL35
Find proteins for P23326 (Spinacia oleracea)
Go to Gene View: RPL35
Go to UniProtKB:  P23326
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36, chloroplastic
f
37Spinacia oleraceaMutation(s): 0 
Gene Names: rpl36
Find proteins for P12230 (Spinacia oleracea)
Go to UniProtKB:  P12230
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
F
221Spinacia oleraceaMutation(s): 0 
Gene Names: RPL3
Find proteins for P82191 (Spinacia oleracea)
Go to Gene View: RPL3
Go to UniProtKB:  P82191
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4, chloroplastic
G
243Spinacia oleraceaMutation(s): 0 
Gene Names: RPL4
Find proteins for O49937 (Spinacia oleracea)
Go to Gene View: RPL4
Go to UniProtKB:  O49937
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5, chloroplastic
H
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: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
I
182Spinacia oleraceaMutation(s): 0 
Gene Names: RPL6
Find proteins for P82193 (Spinacia oleracea)
Go to Gene View: RPL6
Go to UniProtKB:  P82193
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
J
155Spinacia oleraceaMutation(s): 0 
Gene Names: RPL9
Find proteins for P82180 (Spinacia oleracea)
Go to Gene View: RPL9
Go to UniProtKB:  P82180
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein 5 alpha, chloroplastic
g
142Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP5 (RPL40)
Find proteins for P27684 (Spinacia oleracea)
Go to UniProtKB:  P27684
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
a
94Spinacia oleraceaMutation(s): 0 
Gene Names: RPL31
Find proteins for P82249 (Spinacia oleracea)
Go to Gene View: RPL31
Go to UniProtKB:  P82249
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein 6, chloroplastic
h
116Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP6
Find proteins for P82411 (Spinacia oleracea)
Go to UniProtKB:  P82411
Entity ID: 1
MoleculeChainsLengthOrganism
23S rRNAA2810Spinacia oleracea
Entity ID: 2
MoleculeChainsLengthOrganism
Spinach chloroplast 4.5S rRNAC106Spinacia oleracea
Entity ID: 3
MoleculeChainsLengthOrganism
5S rRNAB121Spinacia oleracea
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

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: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-02-08
    Type: Refinement description
  • Version 1.2: 2018-06-06
    Type: Data collection, Other