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 

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:  
    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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32 057Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WH99 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WH99 
Go to UniProtKB:  P9WH99
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 155Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WH95 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WH95 
Go to UniProtKB:  P9WH95
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34 247Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WH93 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WH93 
Go to UniProtKB:  P9WH93
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35 364Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WH91 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WH91 
Go to UniProtKB:  P9WH91
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36 437Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WH89 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WH89 
Go to UniProtKB:  P9WH89
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31 680Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHA1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHA1 
Go to UniProtKB:  P9WHA1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2 C280Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHA5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHA5 
Go to UniProtKB:  P9WHA5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3 D217Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WH87 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WH87 
Go to UniProtKB:  P9WH87
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4 E223Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WH85 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WH85 
Go to UniProtKB:  P9WH85
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5 F187Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WH83 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WH83 
Go to UniProtKB:  P9WH83
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6 G179Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WH81 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WH81 
Go to UniProtKB:  P9WH81
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9 H152Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WH79 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WH79 
Go to UniProtKB:  P9WH79
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13 J147Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHE1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHE1 
Go to UniProtKB:  P9WHE1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14 K122Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHD9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHD9 
Go to UniProtKB:  P9WHD9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15 L146Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHD7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHD7 
Go to UniProtKB:  P9WHD7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16 M138Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHD5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHD5 
Go to UniProtKB:  P9WHD5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17 N180Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHD3 
Go to UniProtKB:  P9WHD3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18 O122Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHD1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHD1 
Go to UniProtKB:  P9WHD1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19 P113Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHC9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHC9 
Go to UniProtKB:  P9WHC9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20 Q129Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHC5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHC5 
Go to UniProtKB:  P9WHC5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
LSU ribosomal protein L21p R104Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHC3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHC3 
Go to UniProtKB:  P9WHC3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22 S197Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHC1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHC1 
Go to UniProtKB:  P9WHC1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23 T100Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHB9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHB9 
Go to UniProtKB:  P9WHB9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24 U105Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHB7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHB7 
Go to UniProtKB:  P9WHB7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25 V215Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHB5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHB5 
Go to UniProtKB:  P9WHB5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27 W86Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHB3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHB3 
Go to UniProtKB:  P9WHB3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28 X64Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045IDB8 (Mycobacterium tuberculosis)
Explore A0A045IDB8 
Go to UniProtKB:  A0A045IDB8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29 Y77Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHA7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHA7 
Go to UniProtKB:  P9WHA7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30 Z65Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WHA3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHA3 
Go to UniProtKB:  P9WHA3
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsLengthOrganismImage
23S rRNAA3138Mycobacterium tuberculosis
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
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

View Full Validation Report



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