7F0D

Cryo-EM structure of Mycobacterium tuberculosis 50S ribosome subunit bound with clarithromycin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Cryo-EM structure of Mycobacterium tuberculosis 50S ribosomal subunit bound with clarithromycin reveals dynamic and specific interactions with macrolides.

Zhang, W.Li, Z.Sun, Y.Cui, P.Liang, J.Xing, Q.Wu, J.Xu, Y.Zhang, W.Zhang, Y.He, L.Gao, N.

(2022) Emerg Microbes Infect 11: 293-305

  • DOI: https://doi.org/10.1080/22221751.2021.2022439
  • Primary Citation of Related Structures:  
    7F0D

  • PubMed Abstract: 

    Tuberculosis (TB) is the leading infectious disease caused by Mycobacterium tuberculosis ( Mtb ). Clarithromycin (CTY), an analog of erythromycin (ERY), is more potent against multidrug-resistance (MDR) TB. ERY and CTY were previously reported to bind to the nascent polypeptide exit tunnel (NPET) near peptidyl transferase center (PTC), but the only available CTY structure in complex with D. radiodurans ( Dra ) ribosome could be misinterpreted due to resolution limitation. To date, the mechanism of specificity and efficacy of CTY for Mtb remains elusive since the Mtb ribosome-CTY complex structure is still unknown. Here, we employed new sample preparation methods and solved the Mtb ribosome-CTY complex structure at 3.3Å with cryo-EM technique, where the crucial gate site A2062 ( E. coli numbering) is located at the CTY binding site within NPET. Two alternative conformations of A2062, a novel syn -conformation as well as a swayed conformation bound with water molecule at interface, may play a role in coordinating the binding of specific drug molecules. The previously overlooked C-H hydrogen bond (H-bond) and π interaction may collectively contribute to the enhanced binding affinity. Together, our structure data provide a structural basis for the dynamic binding as well as the specificity of CTY and explain of how a single methyl group in CTY improves its potency, which provides new evidence to reveal previously unclear mechanism of translational modulation for future drug design and anti-TB therapy. Furthermore, our sample preparation method may facilitate drug discovery based on the complexes with low water solubility drugs by cryo-EM technique.


  • Organizational Affiliation

    Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32A [auth 0]57Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rpmFrpmF_1rpmF_2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33B [auth 1]55Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rpmG2rpmG
UniProt
Find proteins for A5U019 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34C [auth 2]47Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rpmH
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35D [auth 3]64Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rpmI
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36E [auth 4]37Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rpmJ
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31F [auth 6]80Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rpmE
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2I [auth C]280Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplB
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3J [auth D]217Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplC
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4K [auth E]223Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplD
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5L [auth F]187Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplE
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6M [auth G]179Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplF
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9N [auth H]152Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplI
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13O [auth J]147Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplM
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14P [auth K]122Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplN
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15Q [auth L]146Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplO
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16R [auth M]138Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplP
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17S [auth N]180Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplQ
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18T [auth O]122Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplR
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19U [auth P]113Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplS
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20V [auth Q]129Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplT
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21W [auth R]104Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplU
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22X [auth S]197Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplV
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23Y [auth T]100Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplW
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Z [auth U]105Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplX
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25AA [auth V]215Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rplY
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27BA [auth W]86Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rpmA
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28CA [auth X]64Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rpmB
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29DA [auth Y]77Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rpmC
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30EA [auth Z]65Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: rpmD
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Entity ID: 7
MoleculeChains LengthOrganismImage
23S rRNAG [auth A]3,138Mycobacterium tuberculosis H37Ra
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Entity ID: 8
MoleculeChains LengthOrganismImage
5S ribosomal RNAH [auth B]115Mycobacterium tuberculosis H37Ra
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China11179012
National Natural Science Foundation of China (NSFC)China31725007
National Basic Research Program of China (973 Program)China2011CB710800

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release