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 ribosome, solved by cryo-electron microscopy ...

    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 L32A [auth 0]57Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 2
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50S ribosomal protein L33B [auth 1]55Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 3
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50S ribosomal protein L34C [auth 2]47Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 4
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50S ribosomal protein L35D [auth 3]64Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36E [auth 4]37Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 6
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50S ribosomal protein L31F [auth 6]80Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L2I [auth C]280Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 10
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50S ribosomal protein L3J [auth D]217Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L4K [auth E]223Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L5L [auth F]187Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L6M [auth G]179Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L9N [auth H]152Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L13O [auth J]147Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L14P [auth K]122Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L15Q [auth L]146Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16R [auth M]138Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L17S [auth N]180Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L18T [auth O]122Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L19U [auth P]113Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 22
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50S ribosomal protein L20V [auth Q]129Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
LSU ribosomal protein L21pW [auth R]104Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22X [auth S]197Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23Y [auth T]100Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24Z [auth U]105Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25AA [auth V]215Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27BA [auth W]86Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28CA [auth X]64Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
rpmBE5M05_08730E5M52_06825ERS007661_04635ERS007663_03554ERS007665_03011ERS007670_03542ERS007681_04087ERS007683_03718ERS007688_02903ERS007703_04315ERS007720_04214ERS007722_04168ERS007741_02790ERS013440_00118ERS024276_02871ERS027646_03183ERS027659_02720ERS027661_04716FPJ30_16260FPJ31_16405FPJ32_16260FPJ33_16300FPJ34_16260FPJ35_16370FPJ36_16260FPJ37_16240FPJ38_16295FPJ39_16255FPJ40_16255FPJ41_16270FPJ42_16185FPJ43_16250FPJ44_16365FPJ45_16260FPJ46_16255FPJ47_16260FPJ48_16265FPJ49_16255FPJ50_16235FPJ51_16225FPJ52_16330FPJ53_16270FPJ54_16260FPJ55_16425FPJ56_16210FPJ57_16255FPJ58_16255FPJ59_16265FPJ60_16255FPJ61_16260FPJ62_16215FPJ63_16320FPJ64_16370FPJ65_16290FPJ66_16250FPJ67_16325FPJ69_16325FPJ70_16325FPJ71_16320FPJ72_15015FPJ73_16220FPJ76_16235FPJ78_16265FPJ79_16235FPJ80_16340FPJ81_16400FPJ82_16455FPJ83_05310FPJ84_16220FPJ85_05310FPJ86_05310FPJ87_05310FPJ88_16210FPJ89_16300FPJ90_16225FPJ91_16320FPJ92_16240FPJ93_16245FPJ94_15010FPJ95_16250FPJ96_16400FPJ97_16290FPJ98_16270FPJ99_16280FPK00_16185FPK01_16210FPK02_16205FPK03_16210FPK04_16235FPK05_16310FPK06_16175FPK07_16200FPK08_16385FPK09_16375FPK10_14995FPK11_16225FPK12_16190FPK13_16275FPK14_16210FPK16_16200FPK17_16290FPK18_16245FPK19_16285FPK20_16280FPK21_16240FPK22_16255HRD52_15655HRD53_15640SAMEA2683035_02287

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29DA [auth Y]77Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30EA [auth Z]65Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 7
MoleculeChainsLengthOrganismImage
23S rRNAG [auth A]3138Mycobacterium tuberculosis
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Entity ID: 8
MoleculeChainsLengthOrganismImage
5S ribosomal RNAH [auth B]115Mycobacterium tuberculosis
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
917
Query on 917

Download Ideal Coordinates CCD File 
FA [auth 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  (Full details and data files)

  • 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