6O8W

Cryo-EM image reconstruction of the 70S Ribosome Enterococcus faecalis Class01

  • 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: 3.53 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: 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 ...

    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. gerwald_jogl@brown.edu.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth c]204Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKR8 (Enterococcus faecalis)
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Entity ID: 3
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30S ribosomal protein S4C [auth d]201Enterococcus faecalisMutation(s): 0 
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Entity ID: 4
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30S ribosomal protein S5D [auth e]163Enterococcus faecalisMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6E [auth f]97Enterococcus faecalisMutation(s): 0 
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Entity ID: 6
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30S ribosomal protein S7F [auth g]154Enterococcus faecalisMutation(s): 0 
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Entity ID: 7
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30S ribosomal protein S8G [auth h]131Enterococcus faecalisMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth i]128Enterococcus faecalisMutation(s): 0 
Gene Names: rpsICGZ46_14285CUM81_04960DAI13_15990EGW70_09430EU507_05285H9Q64_14800JFI91_06830KUB3007_C26360
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Entity ID: 9
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30S ribosomal protein S10I [auth j]99Enterococcus faecalisMutation(s): 0 
Gene Names: rpsJCGZ46_01200CUM81_00325DAI13_00785EGW70_04350EU507_10330EY666_01600GTI81_10890H9Q64_09070KUB3007_C01360
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Entity ID: 10
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30S ribosomal protein S11J [auth k]117Enterococcus faecalisMutation(s): 0 
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Entity ID: 11
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30S ribosomal protein S12K [auth l]136Enterococcus faecalisMutation(s): 0 
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Entity ID: 12
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30S ribosomal protein S13L [auth m]112Enterococcus faecalisMutation(s): 0 
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Entity ID: 13
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30S ribosomal protein S14 type ZM [auth n]60Enterococcus faecalisMutation(s): 0 
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Entity ID: 14
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30S ribosomal protein S15N [auth o]88Enterococcus faecalisMutation(s): 0 
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Entity ID: 15
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30S ribosomal protein S16O [auth p]89Enterococcus faecalisMutation(s): 0 
Gene Names: rpsPCGZ46_07705CUM81_06195DAI13_08520EU507_02810EY666_03950GTI81_04800H9Q64_02505JFI91_04005KUB3007_C14310
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Entity ID: 16
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30S ribosomal protein S17P [auth q]83Enterococcus faecalisMutation(s): 0 
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Entity ID: 17
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30S ribosomal protein S18Q [auth r]66Enterococcus faecalisMutation(s): 0 
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Entity ID: 18
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30S ribosomal protein S19R [auth s]78Enterococcus faecalisMutation(s): 0 
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Entity ID: 19
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30S ribosomal protein S20S [auth t]81Enterococcus faecalisMutation(s): 0 
Gene Names: rpsTCGZ46_10785CUM81_12095DAI13_12000EGW70_05600EU507_04835EY666_01035GTI81_05750H9Q64_10805JFI91_02660
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Find proteins for A0A1B4XQJ7 (Enterococcus faecalis)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2X [auth C]275Enterococcus faecalisMutation(s): 0 
Gene Names: rplBCGZ46_01220CUM81_00305DAI13_00805EGW70_04370EU507_10350EY666_01580GTI81_10910H9Q64_09050JFI91_05905
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Entity ID: 25
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50S ribosomal protein L3Y [auth D]207Enterococcus faecalisMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L4Z [auth E]206Enterococcus faecalisMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5AA [auth F]177Enterococcus faecalisMutation(s): 0 
Gene Names: rplECGZ46_01265CUM81_00260DAI13_00850EGW70_04415EU507_10395EY666_01535H9Q64_09005JFI91_05950KUB3007_C01490
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Entity ID: 28
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50S ribosomal protein L6BA [auth G]176Enterococcus faecalisMutation(s): 0 
Gene Names: rplFCGZ46_01280CUM81_00245EGW70_04430EU507_10410EY666_01520GTI81_10970H9Q64_08990JFI91_05965KUB3007_C01520
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Entity ID: 29
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50S ribosomal protein L13CA [auth K]145Enterococcus faecalisMutation(s): 0 
Gene Names: rplMCGZ46_14290CUM81_04965DAI13_15995EGW70_09435EU507_05280EY666_14930GTI81_13995H9Q64_14805JFI91_06835
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Entity ID: 30
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50S ribosomal protein L14DA [auth L]122Enterococcus faecalisMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15EA [auth M]146Enterococcus faecalisMutation(s): 0 
Gene Names: rplOCGZ46_01300CUM81_00225DAI13_00885EGW70_04450EU507_10430GTI81_10990H9Q64_08970JFI91_05985KUB3007_C01570
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Entity ID: 32
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50S ribosomal protein L16FA [auth N]141Enterococcus faecalisMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L17GA [auth O]123Enterococcus faecalisMutation(s): 0 
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Entity ID: 34
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50S ribosomal protein L18HA [auth P]117Enterococcus faecalisMutation(s): 0 
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Entity ID: 35
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50S ribosomal protein L19IA [auth Q]114Enterococcus faecalisMutation(s): 0 
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Entity ID: 36
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50S ribosomal protein L20JA [auth R]118Enterococcus faecalisMutation(s): 0 
Gene Names: rplTCGZ46_04015CUM81_07635DAI13_04535EU507_12015EY666_03490H9Q64_06015JFI91_07120KUB3007_C06490
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Entity ID: 37
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50S ribosomal protein L21KA [auth S]102Enterococcus faecalisMutation(s): 0 
Gene Names: rplUCGZ46_04315CUM81_06870DAI13_04805EU507_12375EY666_08665H9Q64_05735JFI91_07380KUB3007_C07000
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Entity ID: 38
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50S ribosomal protein L22LA [auth T]112Enterococcus faecalisMutation(s): 0 
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Entity ID: 39
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50S ribosomal protein L23MA [auth U]89Enterococcus faecalisMutation(s): 0 
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Entity ID: 40
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50S ribosomal protein L24NA [auth V]101Enterococcus faecalisMutation(s): 0 
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Entity ID: 41
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50S ribosomal protein L25OA [auth W]94Enterococcus faecalisMutation(s): 0 
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Entity ID: 42
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50S ribosomal protein L27PA [auth X]76Enterococcus faecalisMutation(s): 0 
Gene Names: rpmACGZ46_04325CUM81_06860DAI13_04815EU507_12385GTI81_01805H9Q64_05725JFI91_07390KUB3007_C07020
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Find proteins for A0A1B4XMB1 (Enterococcus faecalis)
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Entity ID: 43
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50S ribosomal protein L28QA [auth Y]54Enterococcus faecalisMutation(s): 0 
Gene Names: 
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Find proteins for A0A1B4XRZ8 (Enterococcus faecalis)
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Entity ID: 44
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50S ribosomal protein L29RA [auth Z]61Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKV0 (Enterococcus faecalis)
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Entity ID: 45
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50S ribosomal protein L30SA [auth 0]58Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKW1 (Enterococcus faecalis)
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Entity ID: 46
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50S ribosomal protein L31 type BTA [auth 1]59Enterococcus faecalisMutation(s): 0 
Gene Names: rpmE2CGZ46_05435CUM81_06585DAI13_05920EU507_00510EY666_00180GTI81_04295H9Q64_04680JFI91_01955
UniProt
Find proteins for A0A1B4XMV6 (Enterococcus faecalis)
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Entity ID: 47
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50S ribosomal protein L32UA [auth 2]56Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XMM2 (Enterococcus faecalis)
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Entity ID: 48
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50S ribosomal protein L33VA [auth 3]49Enterococcus faecalisMutation(s): 0 
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UniProt
Find proteins for A0A1B4XR98 (Enterococcus faecalis)
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Entity ID: 49
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50S ribosomal protein L34WA [auth 4]44Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XSI4 (Enterococcus faecalis)
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Entity ID: 50
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50S ribosomal protein L35XA [auth 5]64Enterococcus faecalisMutation(s): 0 
Gene Names: rpmICGZ46_04010CUM81_07640DAI13_04530EU507_12010EY666_03485GTI81_01520H9Q64_06020JFI91_07115KUB3007_C06480
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Find proteins for A0A1B4XM73 (Enterococcus faecalis)
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Entity ID: 51
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50S ribosomal protein L36YA [auth 6]38Enterococcus faecalisMutation(s): 0 
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Find proteins for A0A1B4XKT9 (Enterococcus faecalis)
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Entity ID: 1
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16S rRNAA [auth a]1,523Enterococcus faecalis
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Entity ID: 20
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tRNAT [auth u]76Enterococcus faecalis
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Entity ID: 21
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mRNAU [auth v]5Enterococcus faecalis
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Entity ID: 22
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50S subunitV [auth A]2,903Enterococcus faecalis
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Entity ID: 23
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5S rRNAW [auth B]116Enterococcus faecalis
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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