5V7Q

Cryo-EM structure of the large ribosomal subunit from Mycobacterium tuberculosis bound with a potent linezolid analog


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 1.2 of the entry. See complete history

Literature

Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis.

Yang, K.Chang, J.Y.Cui, Z.Li, X.Meng, R.Duan, L.Thongchol, J.Jakana, J.Huwe, C.M.Sacchettini, J.C.Zhang, J.

(2017) Nucleic Acids Res. 45: 10884-10894

  • DOI: 10.1093/nar/gkx785
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the Mtb 50S ribosomal subunit and the complete Mtb 70S ...

    Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the Mtb 50S ribosomal subunit and the complete Mtb 70S ribosome, solved by cryo-electron microscopy. Upon joining of the large and small ribosomal subunits, a 100-nt long expansion segment of the Mtb 23S rRNA, named H54a or the 'handle', switches interactions from with rRNA helix H68 and rProtein uL2 to with rProtein bS6, forming a new intersubunit bridge 'B9'. In Mtb 70S, bridge B9 is mostly maintained, leading to correlated motions among the handle, the L1 stalk and the small subunit in the rotated and non-rotated states. Two new protein densities were discovered near the decoding center and the peptidyl transferase center, respectively. These results provide a structural basis for studying translation in Mtb as well as developing new tuberculosis drugs.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
57Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P9WH99 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WH99
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
55Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpmG2
Find proteins for P9WH95 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WH95
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
47Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpmH
Find proteins for P9WH93 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WH93
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
64Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P9WH91 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WH91
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
37Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P9WH89 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WH89
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
6
80Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpmE
Find proteins for P9WHA1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHA1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
280Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplB
Find proteins for P9WHA5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHA5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
217Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplC
Find proteins for P9WH87 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WH87
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
223Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplD
Find proteins for P9WH85 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WH85
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
187Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplE
Find proteins for P9WH83 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WH83
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
179Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplF
Find proteins for P9WH81 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WH81
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
152Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplI
Find proteins for P9WH79 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WH79
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
147Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplM
Find proteins for P9WHE1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHE1
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
122Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplN
Find proteins for P9WHD9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHD9
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
146Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplO
Find proteins for P9WHD7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHD7
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
138Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplP
Find proteins for P9WHD5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHD5
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
180Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P9WHD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHD3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
122Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplR
Find proteins for P9WHD1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHD1
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
113Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplS
Find proteins for P9WHC9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHC9
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
129Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplT
Find proteins for P9WHC5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHC5
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
LSU ribosomal protein L21p
R
104Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplU
Find proteins for P9WHC3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHC3
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
197Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplV
Find proteins for P9WHC1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHC1
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
100Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplW
Find proteins for P9WHB9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHB9
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
105Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplX
Find proteins for P9WHB7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHB7
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
215Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for P9WHB5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHB5
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
86Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P9WHB3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHB3
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
64Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpmB
Find proteins for A0A045IDB8 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IDB8
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
77Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P9WHA7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHA7
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
65Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P9WHA3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHA3
Entity ID: 7
MoleculeChainsLengthOrganism
23S rRNAA3138Mycobacterium tuberculosis
Entity ID: 8
MoleculeChainsLengthOrganism
5S ribosomal RNAB115Mycobacterium tuberculosis
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
917
Query on 917

Download SDF File 
Download CCD File 
A
N-({(5S)-2-oxo-3-[4-(1,3-thiazol-5-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)acetamide
Llinezolid-114
C15 H15 N3 O3 S
WTZZWIUUAPRUHM-ZDUSSCGKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references
  • Version 1.2: 2017-11-01
    Type: Database references