8KAB

Mycobacterium smegmatis 50S ribosomal subunit-HflX complex


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures reveal the molecular mechanism of HflX-mediated erythromycin resistance in mycobacteria.

Srinivasan, K.Banerjee, A.Sengupta, J.

(2024) Structure 32: 1443

  • DOI: https://doi.org/10.1016/j.str.2024.06.016
  • Primary Citation of Related Structures:  
    8KAB, 8XZ3

  • PubMed Abstract: 

    Mycobacterial HflX confers resistance against macrolide antibiotics. However, the exact molecular mechanism is poorly understood. To gain further insights, we determined the cryo-EM structures of M. smegmatis (Msm) HflX-50S subunit and 50S subunit-erythromycin (ERY) complexes at a global resolution of approximately 3 Å. A conserved nucleotide A2286 at the gate of nascent peptide exit tunnel (NPET) adopts a swayed conformation in HflX-50S complex and interacts with a loop within the linker helical (LH) domain of MsmHflX that contains an additional 9 residues insertion. Interestingly, the swaying of this nucleotide, which is usually found in the non-swayed conformation, is induced by erythromycin binding. Furthermore, we observed that erythromycin decreases HflX's ribosome-dependent GTP hydrolysis, resulting in its enhanced binding and anti-association activity on the 50S subunit. Our findings reveal how mycobacterial HflX senses the presence of macrolides at the peptide tunnel entrance and confers antibiotic resistance in mycobacteria.


  • Organizational Affiliation

    Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein bL37A [auth 3]24Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth C]278Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth D]217Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth E]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth F]187Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth G]179Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9I [auth H]151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10J [auth I]175Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11K [auth J]142Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13L [auth K]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14M [auth L]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15N [auth M]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16O [auth N]138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17P [auth O]199Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18Q [auth P]127Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19R [auth Q]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QV42 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20S [auth R]129Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21T [auth S]103Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22U [auth T]153Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23V [auth U]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24W [auth V]105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25X [auth W]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27Y [auth X]88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28Z [auth Y]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29AA [auth Z]77Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30BA [auth a]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32CA [auth b]57Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 1DA [auth c]55Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34EA [auth d]47Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35FA [auth e]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36GA [auth f]37Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31HA [auth g]75Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase HflXIA [auth h]483Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: hflX
UniProt
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Entity ID: 2
MoleculeChains LengthOrganismImage
23S rRNAB [auth A]3,120Mycolicibacterium smegmatis MC2 155
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth B]118Mycolicibacterium smegmatis MC2 155
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
JA [auth h]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Engineering Research Board (SERB)IndiaCRG/2019/001788
Science and Engineering Research Board (SERB)IndiaSPF/2021/000141

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-09-25
    Changes: Data collection, Database references