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: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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:  
    5V7Q, 5V93

  • 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 ribo ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32 057Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 2
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50S ribosomal protein L33 155Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 3
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50S ribosomal protein L34 247Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 4
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50S ribosomal protein L35 364Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 5
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50S ribosomal protein L36 437Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 6
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50S ribosomal protein L31 680Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L2 C280Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 10
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50S ribosomal protein L3 D217Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L4 E223Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L5 F187Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L6 G179Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L9 H152Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L13 J147Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L14 K122Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L15 L146Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L16 M138Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L17 N180Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L18 O122Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L19 P113Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 22
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50S ribosomal protein L20 Q129Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 23
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LSU ribosomal protein L21p R104Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 24
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50S ribosomal protein L22 S197Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L23 T100Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L24 U105Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25 V215Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L27 W86Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28 X64Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29 Y77Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L30 Z65Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 7
MoleculeChainsLengthOrganismImage
23S rRNAA3138Mycobacterium tuberculosis
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Entity ID: 8
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB115Mycobacterium tuberculosis
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
917
Query on 917
Download Ideal Coordinates CCD File 
A
N-({(5S)-2-oxo-3-[4-(1,3-thiazol-5-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)acetamide
C15 H15 N3 O3 S
WTZZWIUUAPRUHM-ZDUSSCGKSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

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