6W6P

MultiBody Refinement of 70S Ribosome from Enterococcus faecalis

  • Classification: RIBOSOME
  • Organism(s): Enterococcus faecalis OG1RF
  • Mutation(s): No 

  • Deposited: 2020-03-17 Released: 2020-10-14 
  • Deposition Author(s): Jogl, G., Khayat, R.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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-electron microscopy structure of the 70S ribosome from Enterococcus faecalis.

Murphy, E.L.Singh, K.V.Avila, B.Kleffmann, T.Gregory, S.T.Murray, B.E.Krause, K.L.Khayat, R.Jogl, G.

(2020) Sci Rep 10: 16301-16301

  • DOI: https://doi.org/10.1038/s41598-020-73199-6
  • Primary Citation of Related Structures:  
    6O8W, 6O8X, 6O8Y, 6O8Z, 6O90, 6W6P, 6WU9, 6WUA, 6WUB

  • PubMed Abstract: 

    Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to the small ribosomal subunit, assumes different conformations in the five classes, revealing how contacts to the small subunit are maintained throughout intersubunit rotation. A tRNA observed in one of the five classes is positioned in a chimeric pe/E position in a rotated ribosomal state. The 70S ribosome structure of E. faecalis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the development of novel antibiotic compounds effective against this pathogen.


  • Organizational Affiliation

    Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth c]204Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4C [auth d]201Enterococcus faecalis OG1RFMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5D [auth e]163Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6E [auth f]97Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth g]154Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth h]131Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth i]128Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10I [auth j]99Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11J [auth k]117Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12K [auth l]136Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13L [auth m]112Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZM [auth n]60Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15N [auth o]88Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16O [auth p]89Enterococcus faecalis OG1RFMutation(s): 0 
UniProt
Find proteins for A0A1B4XP69 (Enterococcus faecalis)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17P [auth q]83Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18Q [auth r]66Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19R [auth s]78Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20S [auth t]82Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2V [auth C]275Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3W [auth D]207Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4X [auth E]206Enterococcus faecalis OG1RFMutation(s): 0 
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Find proteins for A0A1B4XKU7 (Enterococcus faecalis)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5Y [auth F]177Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6Z [auth G]176Enterococcus faecalis OG1RFMutation(s): 0 
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Find proteins for A0A1B4XKU3 (Enterococcus faecalis)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13AA [auth K]145Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14BA [auth L]122Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15CA [auth M]146Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16DA [auth N]141Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17EA [auth O]124Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18FA [auth P]117Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19GA [auth Q]114Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20HA [auth R]118Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21IA [auth S]102Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22JA [auth T]112Enterococcus faecalis OG1RFMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23KA [auth U]89Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24LA [auth V]101Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27MA [auth X]76Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28NA [auth Y]54Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29OA [auth Z]61Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30PA [auth 0]58Enterococcus faecalis OG1RFMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32QA [auth 2]56Enterococcus faecalis OG1RFMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33RA [auth 3]49Enterococcus faecalis OG1RFMutation(s): 0 
UniProt
Find proteins for A0A1B4XR98 (Enterococcus faecalis)
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UniProt GroupA0A1B4XR98
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34SA [auth 4]44Enterococcus faecalis OG1RFMutation(s): 0 
UniProt
Find proteins for A0A1B4XSI4 (Enterococcus faecalis)
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UniProt GroupA0A1B4XSI4
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35TA [auth 5]64Enterococcus faecalis OG1RFMutation(s): 0 
UniProt
Find proteins for A0A1B4XM73 (Enterococcus faecalis)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36UA [auth 6]38Enterococcus faecalis OG1RFMutation(s): 0 
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Find proteins for A0A1B4XKT9 (Enterococcus faecalis)
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth a]1,548Enterococcus faecalis OG1RF
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Entity ID: 20
MoleculeChains LengthOrganismImage
23S rRNAT [auth A]2,908Enterococcus faecalis OG1RF
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Entity ID: 21
MoleculeChains LengthOrganismImage
5S rRNAU [auth B]116Enterococcus faecalis OG1RF
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14_3235
RECONSTRUCTIONcryoSPARC0.63

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094157
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesG12MD007603

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Refinement description