5O60

Structure of the 50S large ribosomal subunit from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein bL37
3
24Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Find proteins for A0QTP4 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QTP4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
278Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplB
Find proteins for A0QSD4 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
217Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplC
Find proteins for A0QSD1 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD1
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
215Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplD
Find proteins for A0QSD2 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD2
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
187Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplE
Find proteins for A0QSG1 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG1
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
179Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplF
Find proteins for A0QSG4 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG4
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
151Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplI
Find proteins for A0R7F6 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R7F6
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
I
175Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplJ
Find proteins for A0QS62 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS62
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
J
142Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplK
Find proteins for A0QS45 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS45
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
K
147Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplM
Find proteins for A0QSP8 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSP8
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
L
122Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplN
Find proteins for A0QSF9 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSF9
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
M
147Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplO
Find proteins for A0QSG8 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG8
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
N
138Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplP
Find proteins for A0QSD8 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD8
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
O
199Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplQ
Find proteins for A0QSL9 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL9
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
P
127Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplR
Find proteins for A0QSG5 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG5
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
Q
113Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplS
Find proteins for A0QV42 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QV42
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
R
129Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplT
Find proteins for A0QYU6 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QYU6
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
S
103Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplU
Find proteins for A0R151 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R151
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
T
153Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplV
Find proteins for A0QSD6 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD6
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
U
100Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplW
Find proteins for A0QSD3 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD3
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
V
105Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplX
Find proteins for A0QSG0 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG0
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
W
215Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for A0R3D2 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R3D2
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
X
88Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmA
Find proteins for A0R150 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R150
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
Y
64Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmB
Find proteins for A0QV03 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QV03
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Z
77Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmC
Find proteins for A0QSD9 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSD9
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
a
61Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmD
Find proteins for A0QSG7 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSG7
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
57Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmF
Find proteins for A0R3I9 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R3I9
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33 1
c
55Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmG1 (rpmG2)
Find proteins for A0QS39 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QS39
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
d
47Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmH
Find proteins for A0R7K0 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R7K0
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
64Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmI
Find proteins for A0QYU7 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QYU7
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
37Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for A0QSL4 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QSL4
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
g
75Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: rpmE
Find proteins for A0R215 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R215
Entity ID: 2
MoleculeChainsLengthOrganism
23S rRNAA3120Mycolicibacterium smegmatis MC2 155
Entity ID: 3
MoleculeChainsLengthOrganism
5S rRNAB118Mycolicibacterium smegmatis MC2 155
Entity ID: 35
MoleculeChainsLengthOrganism
tRNA CCA-end acetylated (Phe)23Mycolicibacterium smegmatis MC2 155
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
c, f, g, Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PHE
Query on PHE

Download SDF File 
Download CCD File 
2
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
2, A, B, c, C, D, F, N, T
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 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