5O5J

Structure of the 30S small ribosomal subunit from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 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

The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.

Hentschel, J.Burnside, C.Mignot, I.Leibundgut, M.Boehringer, D.Ban, N.

(2017) Cell Rep 20: 149-160

  • DOI: 10.1016/j.celrep.2017.06.029
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of ...

    The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland.,Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Otto-Stern-Weg 5, Zürich 8093, Switzerland. Electronic address: ban@mol.biol.ethz.ch.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Conserved domain protein
B
33Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Find proteins for A0QR10 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QR10
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
C
275Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsC
Find proteins for A0QSD7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
D
201Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsD
Find proteins for A0QSL7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
E
214Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsE
Find proteins for A0QSG6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
F
96Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: rpsF
Find proteins for A0A0D6J3X3 (Mycolicibacterium smegmatis)
Go to UniProtKB:  A0A0D6J3X3
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
G
156Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsG
Find proteins for A0QS97 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS97
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
H
132Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsH
Find proteins for A0QSG3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
I
150Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsI
Find proteins for A0QSP9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSP9
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
J
101Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for A0QSD0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD0
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
K
138Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsK
Find proteins for A0QSL6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL6
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
124Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsL
Find proteins for A0QS96 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS96
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
M
124Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsM
Find proteins for A0QSL5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
N
61Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsZ (rpsN)
Find proteins for A0QSG2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
O
89Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsO
Find proteins for A0QVQ3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QVQ3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
P
156Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsP
Find proteins for A0QV37 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QV37
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Q
98Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for A0QSE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSE0
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18 2
R
84Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsR2 (rpsR1)
Find proteins for A0R7F7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R7F7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S
93Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsS
Find proteins for A0QSD5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD5
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
T
86Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsT
Find proteins for A0R102 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R102
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
V
277Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpsB
Find proteins for A0QVB8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QVB8
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
g
75Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmE
Find proteins for A0R215 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R215
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAA1528Mycolicibacterium smegmatis MC2 155
Entity ID: 22
MoleculeChainsLengthOrganism
tRNA-Phe anticodon stemW19Mycolicibacterium smegmatis MC2 155
Entity ID: 23
MoleculeChainsLengthOrganism
mRNA fragmentX6Mycolicibacterium smegmatis MC2 155
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, F, R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 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
Swiss National Science FoundationSwitzerland310030B_163478
NCCR RNA and disease program, SNSFSwitzerland51NF40_141735

Revision History 

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references
  • Version 1.2: 2018-10-17
    Type: Data collection, Refinement description