6O8X

Cryo-EM image reconstruction of the 70S Ribosome Enterococcus faecalis Class02

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

  • Deposited: 2019-03-12 Released: 2020-09-23 
  • 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: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 faecalisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4C [auth d]201Enterococcus faecalisMutation(s): 0 
UniProt
Find proteins for A0A1B4XRV7 (Enterococcus faecalis)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5D [auth e]163Enterococcus faecalisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6E [auth f]97Enterococcus faecalisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth g]154Enterococcus faecalisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth h]131Enterococcus faecalisMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth i]128Enterococcus faecalisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10I [auth j]99Enterococcus faecalisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11J [auth k]117Enterococcus faecalisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12K [auth l]136Enterococcus faecalisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13L [auth m]112Enterococcus faecalisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZM [auth n]60Enterococcus faecalisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15N [auth o]88Enterococcus faecalisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16O [auth p]89Enterococcus faecalisMutation(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 faecalisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18Q [auth r]66Enterococcus faecalisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19R [auth s]78Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKS0 (Enterococcus faecalis)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20S [auth t]81Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XQJ7 (Enterococcus faecalis)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2V [auth C]275Enterococcus faecalisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3W [auth D]207Enterococcus faecalisMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4X [auth E]206Enterococcus faecalisMutation(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 faecalisMutation(s): 0 
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Find proteins for A0A1B4XKS2 (Enterococcus faecalis)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6Z [auth G]176Enterococcus faecalisMutation(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 faecalisMutation(s): 0 
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Find proteins for A0A1B4XSB2 (Enterococcus faecalis)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14BA [auth L]122Enterococcus faecalisMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15CA [auth M]146Enterococcus faecalisMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16DA [auth N]141Enterococcus faecalisMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17EA [auth O]123Enterococcus faecalisMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18FA [auth P]117Enterococcus faecalisMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19GA [auth Q]114Enterococcus faecalisMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20HA [auth R]118Enterococcus faecalisMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21IA [auth S]102Enterococcus faecalisMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22JA [auth T]112Enterococcus faecalisMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23KA [auth U]89Enterococcus faecalisMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24LA [auth V]101Enterococcus faecalisMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25MA [auth W]94Enterococcus faecalisMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27NA [auth X]76Enterococcus faecalisMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28OA [auth Y]54Enterococcus faecalisMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29PA [auth Z]61Enterococcus faecalisMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30QA [auth 0]58Enterococcus faecalisMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BRA [auth 1]60Enterococcus faecalisMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32SA [auth 2]56Enterococcus faecalisMutation(s): 0 
UniProt
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UniProt GroupA0A1B4XMM2
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33TA [auth 3]49Enterococcus faecalisMutation(s): 0 
UniProt
Find proteins for A0A1B4XR98 (Enterococcus faecalis)
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UniProt GroupA0A1B4XR98
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34UA [auth 4]44Enterococcus faecalisMutation(s): 0 
UniProt
Find proteins for A0A1B4XSI4 (Enterococcus faecalis)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35VA [auth 5]64Enterococcus faecalisMutation(s): 0 
UniProt
Find proteins for A0A1B4XM73 (Enterococcus faecalis)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36WA [auth 6]38Enterococcus faecalisMutation(s): 0 
UniProt
Find proteins for A0A1B4XKT9 (Enterococcus faecalis)
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth a]1,528Enterococcus faecalis
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Entity ID: 20
MoleculeChains LengthOrganismImage
23S rRNAT [auth A]2,903Enterococcus faecalis
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Entity ID: 21
MoleculeChains LengthOrganismImage
5S rRNAU [auth B]116Enterococcus faecalis
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 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

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Refinement description