6HA1

Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader peptide in complex with telithromycin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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 basis for antibiotic resistance mediated by theBacillus subtilisABCF ATPase VmlR.

Crowe-McAuliffe, C.Graf, M.Huter, P.Takada, H.Abdelshahid, M.Novacek, J.Murina, V.Atkinson, G.C.Hauryliuk, V.Wilson, D.N.

(2018) Proc Natl Acad Sci U S A 115: 8978-8983

  • DOI: https://doi.org/10.1073/pnas.1808535115
  • Primary Citation of Related Structures:  
    6HA1, 6HA8

  • PubMed Abstract: 

    Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In Bacillus subtilis , the RPP VmlR confers resistance to lincomycin (Lnc) and the streptogramin A (S A ) antibiotic virginiamycin M (VgM). VmlR is an ATP-binding cassette (ABC) protein of the F type, which, like other antibiotic resistance (ARE) ABCF proteins, is thought to bind to antibiotic-stalled ribosomes and promote dissociation of the drug from its binding site. To investigate the molecular mechanism by which VmlR confers antibiotic resistance, we have determined a cryo-electron microscopy (cryo-EM) structure of an ATPase-deficient B. subtilis VmlR-EQ 2 mutant in complex with a B. subtilis ErmDL-stalled ribosomal complex (SRC). The structure reveals that VmlR binds within the E site of the ribosome, with the antibiotic resistance domain (ARD) reaching into the peptidyltransferase center (PTC) of the ribosome and a C-terminal extension (CTE) making contact with the small subunit (SSU). To access the PTC, VmlR induces a conformational change in the P-site tRNA, shifting the acceptor arm out of the PTC and relocating the CCA end of the P-site tRNA toward the A site. Together with microbiological analyses, our study indicates that VmlR allosterically dissociates the drug from its ribosomal binding site and exhibits specificity to dislodge VgM, Lnc, and the pleuromutilin tiamulin (Tia), but not chloramphenicol (Cam), linezolid (Lnz), nor the macrolide erythromycin (Ery).


  • Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2277Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3209Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4207Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13H [auth J]145Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14I [auth K]122Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15J [auth L]146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16K [auth M]144Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17L [auth N]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18M [auth O]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19N [auth P]115Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20O [auth Q]119Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21P [auth R]102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22Q [auth S]113Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23R [auth T]95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24S [auth U]103Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27T [auth W]94Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28U [auth X]62Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29V [auth Y]66Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30W [auth Z]59Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32X [auth 0]59Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 1Y [auth 1]49Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34Z [auth 2]44Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35AA [auth 3]66Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36BA [auth 4]37Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31CA [auth 6]63Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2FA [auth b]246Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3GA [auth c]218Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4HA [auth d]200Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5IA [auth e]166Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6JA [auth f]95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7KA [auth g]156Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8LA [auth h]132Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9MA [auth i]130Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10NA [auth j]102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11OA [auth k]131Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12PA [auth l]138Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13QA [auth m]121Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14RA [auth n]61Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15SA [auth o]89Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16TA [auth p]90Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17UA [auth q]87Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18VA [auth r]79Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19WA [auth s]92Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
UniProt
Find proteins for P21476 (Bacillus subtilis (strain 168))
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Go to UniProtKB:  P21476
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UniProt GroupP21476
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20XA [auth t]88Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
UniProt
Find proteins for P21477 (Bacillus subtilis (strain 168))
Explore P21477 
Go to UniProtKB:  P21477
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UniProt GroupP21477
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNA2,928Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNA112Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 30
MoleculeChains LengthOrganismImage
mRNADA [auth 7]3Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 31
MoleculeChains LengthOrganismImage
16S ribosomal RNAEA [auth a]1,554Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 51
MoleculeChains LengthOrganismImage
P-tRNAYA [auth x]87Escherichia coli
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TEL
Query on TEL

Download Ideal Coordinates CCD File 
ZA [auth A]TELITHROMYCIN
C43 H65 N5 O10
LJVAJPDWBABPEJ-PNUFFHFMSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIXdev-2947-000

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR1805
German Research FoundationGermanyWI3285/6-1
Ministry of Education (Czech Republic)Czech RepublicCIISB project number LM2015043
European UnionCzech RepubliciNext project number 2992

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Other
  • Version 1.3: 2021-01-27
    Changes: Data collection, Structure summary