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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32A [auth 0]57Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33B [auth 1]55Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34C [auth 2]47Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35D [auth 3]64Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36E [auth 4]37Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31F [auth 6]80Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2I [auth C]280Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3J [auth D]217Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4K [auth E]223Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5L [auth F]187Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6M [auth G]179Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9N [auth H]152Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13O [auth J]147Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14P [auth K]122Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15Q [auth L]146Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16R [auth M]138Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17S [auth N]180Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18T [auth O]122Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19U [auth P]113Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20V [auth Q]129Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
LSU ribosomal protein L21pW [auth R]104Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22X [auth S]197Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23Y [auth T]100Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Z [auth U]105Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25AA [auth V]215Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27BA [auth W]86Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28CA [auth X]64Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29DA [auth Y]77Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30EA [auth Z]65Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
CapreomycinGA [auth b]6Streptomyces californicusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3HA [auth c]274Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4IA [auth d]201Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5JA [auth e]220Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6KA [auth f]96Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7LA [auth g]156Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8MA [auth h]132Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9NA [auth i]151Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10OA [auth j]101Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11PA [auth k]139Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12QA [auth l]124Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13RA [auth m]124Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZSA [auth n]61Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15TA [auth o]89Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16UA [auth p]162Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17VA [auth q]135Mycobacterium tuberculosisMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18WA [auth r]84Mycobacterium tuberculosisMutation(s): 0 
UniProt
Find proteins for P9WH49 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WH49
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19XA [auth s]93Mycobacterium tuberculosisMutation(s): 0 
UniProt
Find proteins for P9WH45 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WH45
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20YA [auth t]86Mycobacterium tuberculosisMutation(s): 0 
UniProt
Find proteins for P9WH41 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial domain of uncharacterised function (DUF1713)ZA [auth x]33Mycobacterium tuberculosisMutation(s): 0 
UniProt
Find proteins for P9WKT5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WKT5
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Entity ID: 7
MoleculeChains LengthOrganismImage
23S rRNAG [auth A]3,138Mycobacterium tuberculosis
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Entity ID: 8
MoleculeChains LengthOrganismImage
5S rRNAH [auth B]115Mycobacterium tuberculosis
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Entity ID: 32
MoleculeChains LengthOrganismImage
16S rRNAFA [auth a]1,537Mycobacterium tuberculosis
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Small Molecules
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
DPP
Query on DPP		GA [auth b]L-PEPTIDE LINKINGC3 H8 N2 O2ALA
KBE
Query on KBE		GA [auth b]L-PEPTIDE LINKINGC6 H14 N2 O2LYS
MYN
Query on MYN		GA [auth b]L-PEPTIDE LINKINGC6 H12 N4 O2ARG
Biologically Interesting Molecules (External Reference) 1 Unique
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  (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
  • Version 1.3: 2020-08-12
    Changes: Database references, Derived calculations, Structure summary