5V93

Cryo-EM structure of the 70S ribosome from Mycobacterium tuberculosis bound with Capreomycin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 ...

    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 L32057Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A045IMI5 (Mycobacterium tuberculosis)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33155Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045HU86 (Mycobacterium tuberculosis)
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Entity ID: 3
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50S ribosomal protein L34247Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35364Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045KKY9 (Mycobacterium tuberculosis)
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Entity ID: 5
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50S ribosomal protein L36437Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31680Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A045HLX7 (Mycobacterium tuberculosis)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C280Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A045H5T7 (Mycobacterium tuberculosis)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3D217Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4E223Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5F187Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L6G179Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L9H152Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13J147Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A0T9D5H2 (Mycobacterium tuberculosis)
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Entity ID: 16
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50S ribosomal protein L14K122Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L15L146Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplOERS007688_04067
Find proteins for A0A654TTE7 (Mycobacterium tuberculosis)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16M138Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L17N180Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18O122Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A045JK28 (Mycobacterium tuberculosis)
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Entity ID: 21
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50S ribosomal protein L19P113Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 22
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50S ribosomal protein L20Q129Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 23
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LSU ribosomal protein L21pR104Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 24
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50S ribosomal protein L22S197Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L23T100Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L24U105Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 27
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50S ribosomal protein L25V215Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L27W86Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A045K0G1 (Mycobacterium tuberculosis)
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Entity ID: 29
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50S ribosomal protein L28X64Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L29Y77Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A045IQ64 (Mycobacterium tuberculosis)
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Entity ID: 31
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50S ribosomal protein L30Z65Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Capreomycinb6Streptomyces californicusMutation(s): 0 
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Entity ID: 34
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30S ribosomal protein S3c274Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 35
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30S ribosomal protein S4d201Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5e220Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A045JKV0 (Mycobacterium tuberculosis)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6f96Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A045JVY9 (Mycobacterium tuberculosis)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7g156Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8h132Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A045IWX2 (Mycobacterium tuberculosis)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9i151Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 41
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30S ribosomal protein S10j101Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A045HTN2 (Mycobacterium tuberculosis)
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Entity ID: 42
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30S ribosomal protein S11k139Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 43
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30S ribosomal protein S12l124Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 44
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30S ribosomal protein S13m124Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 45
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30S ribosomal protein S14 type Zn61Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 46
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30S ribosomal protein S15o89Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 47
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30S ribosomal protein S16p162Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 48
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30S ribosomal protein S17q135Mycobacterium tuberculosisMutation(s): 0 
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Find proteins for A0A0E9AP91 (Mycobacterium tuberculosis)
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Entity ID: 49
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30S ribosomal protein S18r84Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 50
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30S ribosomal protein S19s93Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 51
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30S ribosomal protein S20t86Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 52
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Mitochondrial domain of uncharacterised function (DUF1713)x33Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 7
MoleculeChainsLengthOrganismImage
23S rRNAA3138Mycobacterium tuberculosis
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Entity ID: 8
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5S rRNAB115Mycobacterium tuberculosis
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Entity ID: 32
MoleculeChainsLengthOrganismImage
16S rRNAa1537Mycobacterium tuberculosis
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
DPP
Query on DPP
bL-PEPTIDE LINKINGC3 H8 N2 O2ALA
KBE
Query on KBE
bL-PEPTIDE LINKINGC6 H14 N2 O2LYS
MYN
Query on MYN
bL-PEPTIDE LINKINGC6 H12 N4 O2ARG
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 33
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002272
Query on PRD_002272
bCapreomycin 1BCyclic peptide /  Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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
  • Version 1.3: 2020-08-12
    Changes: Database references, Derived calculations, Structure summary