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- EMDB-21908: 30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBod... -

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Basic information

Entry
Database: EMDB / ID: EMD-21908
Title30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBody refinement
Map data30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBody refinement
Sample
  • Complex: Enterococcus faecalis
    • RNA: 16S rRNA
    • Protein or peptide: 30S ribosomal protein S3
    • Protein or peptide: 30S ribosomal protein S7
    • Protein or peptide: 30S ribosomal protein S9
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S13
    • Protein or peptide: 30S ribosomal protein S14 type ZRibosome
    • Protein or peptide: 30S ribosomal protein S19
  • Ligand: ZINC ION
Keywords70S / ribosome / pathogen / antibiotic development / antibiotic resistant
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Type-1 KH domain profile. / Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / K Homology domain / K homology RNA-binding domain ...Type-1 KH domain profile. / Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S14 / Type-2 KH domain profile. / Ribosomal protein S13/S18 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S13-like, H2TH / Ribosomal protein S9, conserved site / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S13 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S13 family profile. / Ribosomal protein S10p/S20e / Ribosomal protein S9 / Ribosomal protein S7p/S5e / Ribosomal protein S9/S16 / Ribosomal protein S9 signature. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS14C ...Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS14C / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7
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-6wua
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21908.png

Downloads & links

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Map

FileDownload / File: emd_21908.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation30S subunit (head) 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-0.03963051 - 0.116611235
Average (Standard dev.)-0.0009723742 (±0.003378916)
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-0.0400.117-0.001

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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 S3
    • Protein or peptide: 30S ribosomal protein S7
    • Protein or peptide: 30S ribosomal protein S9
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S13
    • Protein or peptide: 30S ribosomal protein S14 type ZRibosome
    • Protein or peptide: 30S ribosomal protein S19
  • Ligand: ZINC ION

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Supramolecule #1: Enterococcus faecalis

SupramoleculeName: Enterococcus faecalis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
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 S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 22.884309 KDa
SequenceString: GQKVHPIGMR VGIIRDWDAK WYAEKEYAEF LHEDLRIRKF IATKLADAAV STIEIERAAN RVNISIHTAK PGMVIGKGGS EVENLRKEL NKLTGKRVHI NIVEIKKPDL DAKLVGEGIA RQLENRVAFR RAQKQAIQRA MRAGAKGIKT QVSGRLNGAD I ARSEGYSE ...String:
GQKVHPIGMR VGIIRDWDAK WYAEKEYAEF LHEDLRIRKF IATKLADAAV STIEIERAAN RVNISIHTAK PGMVIGKGGS EVENLRKEL NKLTGKRVHI NIVEIKKPDL DAKLVGEGIA RQLENRVAFR RAQKQAIQRA MRAGAKGIKT QVSGRLNGAD I ARSEGYSE GTVPLHTLRA DIDYAWEEAD TTYGKLGVKV WIYRGE

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #3: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 17.547219 KDa
SequenceString:
PRKGPVAKRD VLPDPIYNSK LVTRLINRVM VDGKRGIAAN IIYNSFDIIK ESTGNDPLEV FEQAMKNVMP VLEVKARRVG GSNYQVPVE VRPERRTTLG LRWVVNYARL RGEHTMEERL AKEIMDAANN TGASVKKRED THKMADANRA FAHYR

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #4: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 14.069206 KDa
SequenceString:
QVQYSGTGRR KNAVARVRLV PGTGKITVNK KDVEEYIPHA DLREVINQPF GVTETKGAYD VIVNVNGGGY AGQSGAIRHG IARALLQVD PDFRSALKRA GLLTRDARMV ERKKPGLKKA RKASQFSKR

UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #5: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 11.400286 KDa
SequenceString:
QKIRIRLKAY EHRILDQSAD KIVETAKRTG ADVSGPIPLP TERSLYTVIR ATHKYKDSRE QFEMRTHKRL IDIVNPTPKT VDALMKLDL PSGVNIEIKL

UniProtKB: Small ribosomal subunit protein uS10

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Macromolecule #6: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 12.619492 KDa
SequenceString:
ARIAGVDIPR DKRVVVSLTY IYGIGNTTAK KVLANVGVSE DVRVRDLTNE QTDAIRAEID KLKVEGDLRR EVNLNIKRLM EIGSYRGIR HRRGLPTRGQ NTKNNARTRK GPT

UniProtKB: Small ribosomal subunit protein uS13

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Macromolecule #7: 30S ribosomal protein S14 type Z

MacromoleculeName: 30S ribosomal protein S14 type Z / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 7.041397 KDa
SequenceString:
AKKSMIAKNK RPAKHSTQAY TRCERCGRPH SVYRKFHLCR ICFRELAYKG QIPGVKKASW

UniProtKB: Small ribosomal subunit protein uS14

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Macromolecule #8: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 8.999471 KDa
SequenceString:
SLKKGPFVDD HLMKKVEAQQ GAEKKKVIKT WSRRSTIFPS FVGFTIAVYD GRKHVPVYIQ EDMVGHKLGE FAPTRTYR

UniProtKB: Small ribosomal subunit protein uS19

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 277 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Initial angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 0.63)
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

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

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