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- EMDB-21909: 30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBod... -

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Basic information

Entry
Database: EMDB / ID: EMD-21909
Title30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBody refinement
Map data30S subunit (body) of 70S Ribosome Enterococcus faecalis MultiBody refinement
Sample
  • Complex: Enterococcus faecalis
    • RNA: x 1 types
    • Protein or peptide: x 11 types
Keywords70S / ribosome / pathogen / antibiotic development / antibiotic resistant
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. ...Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S11 / Ribosomal protein S11 / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS4 ...Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesEnterococcus faecalis OG1RF (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJogl G / Khayat R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094157 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)G12MD007603 United States
CitationJournal: Sci Rep / Year: 2020
Title: Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis.
Authors: Eileen L Murphy / Kavindra V Singh / Bryant Avila / Torsten Kleffmann / Steven T Gregory / Barbara E Murray / Kurt L Krause / Reza Khayat / Gerwald Jogl /
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 ...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.
History
DepositionMay 4, 2020-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wub
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21909.png

Downloads & links

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Map

FileDownload / File: emd_21909.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation30S subunit (body) of 70S Ribosome Enterococcus faecalis MultiBody refinement
Voxel sizeX=Y=Z: 1.097 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.06811923 - 0.17649846
Average (Standard dev.)-0.00074154173 (±0.0053954916)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 482.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0971.0971.097
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z482.680482.680482.680
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0680.176-0.001

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Supplemental data

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Sample components

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Entire : Enterococcus faecalis

EntireName: Enterococcus faecalis (bacteria)
Components
  • Complex: Enterococcus faecalis
    • RNA: 16S rRNA
    • Protein or peptide: 30S ribosomal protein S4
    • Protein or peptide: 30S ribosomal protein S5
    • Protein or peptide: 30S ribosomal protein S6
    • Protein or peptide: 30S ribosomal protein S8
    • Protein or peptide: 30S ribosomal protein S11
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S15
    • Protein or peptide: 30S ribosomal protein S16
    • Protein or peptide: 30S ribosomal protein S17
    • Protein or peptide: 30S ribosomal protein S18
    • Protein or peptide: 30S ribosomal protein S20

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Supramolecule #1: Enterococcus faecalis

SupramoleculeName: Enterococcus faecalis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 2.5 MDa

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Macromolecule #1: 16S rRNA

MacromoleculeName: 16S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 501.090781 KDa
SequenceString: UGAGAGUUUG AUCCUGGCUC AGGACGAACG CUGGCGGCGU GCCUAAUACA UGCAAGUCGA ACGCUUCUUU CCUCCCGAGU GCUUGCACU CAAUUGGAAA GAGGAGUGGC GGACGGGUGA GUAACACGUG GGUAACCUAC CCAUCAGAGG GGGAUAACAC U UGGAAACA ...String:
UGAGAGUUUG AUCCUGGCUC AGGACGAACG CUGGCGGCGU GCCUAAUACA UGCAAGUCGA ACGCUUCUUU CCUCCCGAGU GCUUGCACU CAAUUGGAAA GAGGAGUGGC GGACGGGUGA GUAACACGUG GGUAACCUAC CCAUCAGAGG GGGAUAACAC U UGGAAACA GGUGCUAAUA CCGCAUAACA GUUUAUGCCG CAUGGCAUAA GAGUGAAAGG CGCUUUCGGG UGUCGCUGAU GG AUGGACC CGCGGUGCAU UAGCUAGUUG GUGAGGUAAC GGCUCACCAA GGCCACGAUG CAUAGCCGAC CUGAGAGGGU GAU CGGCCA CACUGGGACU GAGACACGGC CCAGACUCCU ACGGGAGGCA GCAGUAGGGA AUCUUCGGCA AUGGACGAAA GUCU GACCG AGCAACGCCG CGUGAGUGAA GAAGGUUUUC GGAUCGUAAA ACUCUGUUGU UAGAGAAGAA CAAGGACGUU AGUAA CUGA ACGUCCCCUG ACGGUAUCUA ACCAGAAAGC CACGGCUAAC UACGUGCCAG CAGCCGCGGU AAUACGUAGG UGGCAA GCG UUGUCCGGAU UUAUUGGGCG UAAAGCGAGC GCAGGCGGUU UCUUAAGUCU GAUGUGAAAG CCCCCGGCUC AACCGGG GA GGGUCAUUGG AAACUGGGAG ACUUGAGUGC AGAAGAGGAG AGUGGAAUUC CAUGUGUAGC GGUGAAAUGC GUAGAUAU A UGGAGGAACA CCAGUGGCGA AGGCGGCUCU CUGGUCUGUA ACUGACGCUG AGGCUCGAAA GCGUGGGGAG CAAACAGGA UUAGAUACCC UGGUAGUCCA CGCCGUAAAC GAUGAGUGCU AAGUGUUGGA GGGUUUCCGC CCUUCAGUGC UGCAGCAAAC GCAUUAAGC ACUCCGCCUG GGGAGUACGA CCGCAAGGUU GAAACUCAAA GGAAUUGACG GGGGCCCGCA CAAGCGGUGG A GCAUGUGG UUUAAUUCGA AGCAACGCGA AGAACCUUAC CAGGUCUUGA CAUCCUUUGA CCACUCUAGA GAUAGAGCUU UC CCUUCGG GGACAAAGUG ACAGGUGGUG CAUGGUUGUC GUCAGCUCGU GUCGUGAGAU GUUGGGUUAA GUCCCGCAAC GAG CGCAAC CCUUAUUGUU AGUUGCCAUC AUUUAGUUGG GCACUCUAGC GAGACUGCCG GUGACAAACC GGAGGAAGGU GGGG AUGAC GUCAAAUCAU CAUGCCCCUU AUGACCUGGG CUACACACGU GCUACAAUGG GAAGUACAAC GAGUCGCUAG ACCGC GAGG UCAUGCAAAU CUCUUAAAGC UUCUCUCAGU UCGGAUUGCA GGCUGCAACU CGCCUGCAUG AAGCCGGAAU CGCUAG UAA UCGCGGAUCA GCACGCCGCG GUGAAUACGU UCCCGGGCCU UGUACACACC GCCCGUCACA CCACGAGAGU UUGUAAC AC CCGAAGUCGG UGAGGUAACC UUUUUGGAGC CAGCCGCCUA AGGUGGGAUA GAUGAUUGGG GUGAAGUCGU AACAAGGU A GCCGUAUCGG AAGGUGCGGC UGGAUCA

GENBANK: GENBANK: CP002621.1

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Macromolecule #2: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 23.029299 KDa
SequenceString: SRYTGPSWKV SRRLGISLSG TGKELARRPY KPGQHGPNSR GKVSEYGMQL TEKQKLRHMY GMNERQFRTL FIKASKIKEG KHGVNFMVL LEQRLDNVVY RLGLATTRRQ ARQLVNHGHI TVDGKRVDIP SYHVEVGQVI GVREKSQNIS TIKEAVEATV G RPAFVSFD ...String:
SRYTGPSWKV SRRLGISLSG TGKELARRPY KPGQHGPNSR GKVSEYGMQL TEKQKLRHMY GMNERQFRTL FIKASKIKEG KHGVNFMVL LEQRLDNVVY RLGLATTRRQ ARQLVNHGHI TVDGKRVDIP SYHVEVGQVI GVREKSQNIS TIKEAVEATV G RPAFVSFD TEKLEGSFTR LPERDELYPE IDEALVVEYY NQK

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #3: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 17.156979 KDa
SequenceString:
YIDPKHLELE DRVVAINRVT KVVKGGRRLR FAALVVVGDK NGHVGFGTGK AQEVPEAIRK AIEDAKKNLV EVPMVGSTIP HEVIGVFGG GRILMKPAVE GSGVAAGGPV RAVLELAGVA DITSKSLGSN TPINVVRATV EGLKQLKRAE EVAALRGKSV E EII

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #4: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 11.331838 KDa
SequenceString:
QDTKYEIMYI IRPNIDEEAK TALVERFDTI LKDNGAEVIE SKDWEKRRLA YEMNGFREGI YHIVNVTSPS TAGAINEFDR LAKINDDII RHMIVKVE

UniProtKB: Small ribosomal subunit protein bS6

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Macromolecule #5: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 14.805198 KDa
SequenceString:
VMTDPIADFL TRIRNANMVK HETLEVPASK IKRDIAEILK REGFIRDVEY IEDDKQGVIR VFLKYGKNEE RVITNLKRIS KPGLRAYVK ADEVPKVLNG LGIAIISTSE GVITDKEARA KNIGGEVIAY VW

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #6: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 12.3221 KDa
SequenceString:
KKNIESGVAH IHSTFNNTIV MITDTHGNAL AWSSAGSLGF KGSKKSTPFA AQMAAEAATK VAMEHGLKTV DVTVKGPGSG REAAIRSLQ ATGLEVTAIR DVTPVPHNGC RPPKRRRV

UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #7: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 15.178622 KDa
SequenceString:
PTINQLVRKP RKSKVEKSDS PALNKGYNSF KKTQTNVNSP QKRGVCTRVG TMTPKKPNSA LRKYARVRLS NLIEVTAYIP GIGHNLQEH SVVLLRGGRV KDLPGVRYHI VRGALDTAGV NDRKQSRSKY GTKRPKA

UniProtKB: Small ribosomal subunit protein uS12

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Macromolecule #8: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 10.537042 KDa
SequenceString:
AISQERKNEI IKEYARHEGD TGSPEVQIAV LTEDINQLNE HARTHKKDHH SYRGLMKKIG HRRNLLAYLR KTDIQRYREL IQRLGLRR

UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #9: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 10.095773 KDa
SequenceString:
AVKIRLKRMG SKKSPFYRIV VADSRSPRDG RFIETVGTYN PLKDPAEVVL KEDLVLDWLS KGAQPSDTVR NILSKEGVMK KHHEAKNVK

UniProtKB: Small ribosomal subunit protein bS16

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Macromolecule #10: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 9.74437 KDa
SequenceString:
ERNQRKVYQG RVVSDKMDKT ITVVVETKKN HPIYGKRMKY SKKYKAHDEN NTAKVGDIVK IMETRPLSAT KRFRLLEVVE EAV

UniProtKB: Small ribosomal subunit protein uS17

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Macromolecule #11: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 7.646979 KDa
SequenceString:
KVDYIAANHI EYIDYKDTEL LKRFISERGK ILPRRVTGTG AKNQRKLTIA IKRARIMGLL PFVSDE

UniProtKB: Small ribosomal subunit protein bS18

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Macromolecule #12: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 8.841125 KDa
SequenceString:
PNIESAIKRV RTSANANAKN SSQTNAMRTA IKKFEEAVAA GADNVDALYN EAVKAVDMAA TKGLIHKNKA NRDKIRLSKL AK

UniProtKB: Small ribosomal subunit protein bS20

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV
Details: Vol = 4 uL, BT = 4 sec, BF = 0, DT = 0, WT = 8 sec.
DetailsSample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.63) / Number images used: 335675
Initial angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 0.63)

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Atomic model buiding 1

Initial model
PDB IDChain

5li0

source_name: PDB, initial_model_type: experimental model

4ybb

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 177 / Target criteria: Correlation Coefficient
Output model

PDB-6wub:
30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBody refinement

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