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- EMDB-21907: 50S subunit of 70S Ribosome Enterococcus faecalis MultiBody refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-21907
Title50S subunit of 70S Ribosome Enterococcus faecalis MultiBody refinement
Map data50S subunit of 70S Ribosome Enterococcus faecalis MultiBody refinement
Sample
  • Complex: Enterococcus faecalis
    • RNA: x 2 types
    • Protein or peptide: x 25 types
  • Ligand: x 1 types
Keywords70S / ribosome / pathogen / antibiotic development / antibiotic resistant
Function / homology
Function and homology information


ribosomal large subunit assembly / large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type ...Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L30 signature. / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L29 signature. / Ribosomal protein L5 / Ribosomal protein L6, alpha-beta domain / ribosomal L5P family C-terminus / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L6 / Ribosomal protein L14P, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L22/L17, conserved site / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal L29 protein / Ribosomal protein L24/L26, conserved site
Similarity search - Domain/homology
Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 ...Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL33C / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32C / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3
Similarity search - Component
Biological speciesEnterococcus faecalis OG1RF (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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
  • Download
  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wu9
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21907.png

Downloads & links

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Map

FileDownload / File: emd_21907.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation50S subunit 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-0.0851723 - 0.2261516
Average (Standard dev.)-0.00046657008 (±0.009041678)
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-0.0850.226-0.000

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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: 23S rRNA23S ribosomal RNA
    • RNA: 5S rRNA5S ribosomal RNA
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
  • Ligand: ZINC ION

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Supramolecule #1: Enterococcus faecalis

SupramoleculeName: Enterococcus faecalis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#27
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 2.5 MDa

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Macromolecule #1: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 942.67575 KDa
SequenceString: UUAAGUGAAU AAGGGCGCAC GGUGGAUGCC UUGGCACUAG GAGCCGAUGA AGGACGGGAC UAACACCGAU AUGCUUUGGG GAGCUGUAA GUAAGCUAUG AUCCAGAGAU UUCCGAAUGG GGGAACCCAA UAUCUUUUAU AGGAUAUUAC UUUUCAGUGA A UACAUAGC ...String:
UUAAGUGAAU AAGGGCGCAC GGUGGAUGCC UUGGCACUAG GAGCCGAUGA AGGACGGGAC UAACACCGAU AUGCUUUGGG GAGCUGUAA GUAAGCUAUG AUCCAGAGAU UUCCGAAUGG GGGAACCCAA UAUCUUUUAU AGGAUAUUAC UUUUCAGUGA A UACAUAGC UGAUUAGAGG UAGACGCAGA GAACUGAAAC AUCUUAGUAC CUGCAGGAAG AGAAAGAAAA UUCGAUUCCC UG AGUAGCG GCGAGCGAAA CGGGAAGAGC CCAAACCAAC AAGCUUGCUU GUUGGGGUUG UAGGACUCCG AUAUGGUAGU CUG UUAGUA UAGUUGAAGG AUUUGGAAAA UUCCGCUAAA GAGGGUGAAA GCCCCGUAGA CGAAAUGCUG ACAACACCUA GGAG GAUCC UGAGUACGGC GGAACACGAG AAAUUCCGUC GGAAUCCGCG GGGACCAUCC CGCAAGGCUA AAUACUCCCU AGUGA CCGA UAGUGAACCA GUACCGUGAG GGAAAGGUGA AAAGCACCCC GGAAGGGGAG UGAAAUAGAU CCUGAAACCG UGUGCC UAC AACAAGUCAA AGCUCGUUAA UGAGUGAUGG CGUGCCUUUU GUAGAAUGAA CCGGCGAGUU ACGAUUGCAU GCGAGGU UA AGUCGAAGAG ACGGAGCCGC AGCGAAAGCG AGUCUGAAUA GGGCGAAUGA GUAUGUAGUC GUAGACCCGA AACCAUGU G AUCUACCCAU GUCCAGGUUG AAGGUGCGGU AAAACGCACU GGAGGACCGA ACCCACGUAC GUUGAAAAGU GCGGGGAUG AGGUGUGGGU AGCGGAGAAA UUCCAAACGA ACUUGGAGAU AGCUGGUUCU CUCCGAAAUA GCUUUAGGGC UAGCCUCGGA AUUGAGAAU GAUGGAGGUA GAGCACUGUU UGGACUAGGG GCCCAUCUCG GGUUACCGAA UUCAGAUAAA CUCCGAAUGC C AUUCAUUU AUAUCCGGGA GUCAGACUGC GAGUGAUAAG AUCCGUAGUC GAAAGGGAAA CAGCCCAGAC CACCAGCUAA GG UCCCAAA AUAUAUGUUA AGUGGAAAAG GAUGUGGGGU UGCACAGACA ACUAGGAUGU UGGCUUAGAA GCAGCCACCA UUU AAAGAG UGCGUAAUAG CUCACUAGUC GAGUGACCCU GCGCCGAAAA UGUACCGGGG CUAAACAUAU UACCGAAGCU GUGG ACUAC ACCAUUAGGU GUAGUGGUAG GAGAGCGUUC UAAGGGCGUU GAAGGUCGAU CGUGAGGACG GCUGGAGCGC UUAGA AGUG AGAAUGCCGG UAUGAGUAGC GAAAGACAGG UGAGAAUCCU GUCCACCGUA UGACUAAGGU UUCCUGGGGA AGGCUC GUC CGCCCAGGGU UAGUCGGGAC CUAAGCCGAG GCCGAUAGGC GUAGGCGAUG GACAACAGGU UGAUAUUCCU GUACCAG UU GUUUUUGUUU GAGCAAUGGA GGGACGCAGU AGGCUAAGGA AUGCAUGCGA UUGGAAGUGC AUGUCCAAGC AAUGAGUC U UGAGUAGAGU UAAAUGCUUU ACUCUUUAAG GACAAGUUGU GACGGGGAGC GAAAUAAUAG UAGCGAAGUU CCUGACGUC ACACUGCCAA GAAAAGCUUC UAGUGAGAAA ACAACUGCCC GUACCGUAAA CCGACACAGG UAGUCGAGGA GAGUAUCCUA AGGUGAGCG AGCGAACUCU CGUUAAGGAA CUCGGCAAAA UGACCCCGUA ACUUCGGGAG AAGGGGUGCU GACUUCGGUC A GCCGCAGU GAAUAGGCCC AAGCGACUGU UUAUCAAAAA CACAGGUCUC UGCAAAAUCG UAAGAUGAAG UAUAGGGGCU GA CGCCUGC CCGGUGCUGG AAGGUUAAGA GGAUGGGUUA GCUUCGGCGA AGCUCAGAAU UGAAGCCCCA GUAAACGGCG GCC GUAACU AUAACGGUCC UAAGGUAGCG AAAUUCCUUG UCGGGUAAGU UCCGACCCGC ACGAAAGGCG UAACGAUUUG GGCA CUGUC UCAACGAGAG ACUCGGUGAA AUUUUAGUAC CUGUGAAGAU GCAGGUUACC CGCGACAGGA CGGAAAGACC CCAUG GAGC UUUACUGUAG UUUGAUAUUG AGUGUUUGUA CCACAUGUAC AGGAUAGGUA GGAGCCGAUG AGACCGGAAC GCUAGU UUC GGAGGAGGCG CUGGUGGGAU ACUACCCUUG UGUUAUGAAC CCUCUAACCC GCACCACUAA UCGUGGUGGG AGACAGU GU CAGAUGGGCA GUUUGACUGG GGCGGUCGCC UCCUAAAAGG UAACGGAGGC GCCCAAAGGU UCCCUCAGAA UGGUUGGA A AUCAUUCGAA GAGUGUAAAG GCAGAAGGGA GCUUGACUGC GAGACCUACA AGUCGAGCAG GGACGAAAGU CGGGCUUAG UGAUCCGGUG GUUCCGCAUG GAAGGGCCAU CGCUCAACGG AUAAAAGCUA CCCUGGGGAU AACAGGCUUA UCUCCCCCAA GAGUCCACA UCGACGGGGA GGUUUGGCAC CUCGAUGUCG GCUCGUCGCA UCCUGGGGCU GUAGUCGGUC CCAAGGGUUG G GCUGUUCG CCCAUUAAAG CGGCACGCGA GCUGGGUUCA GAACGUCGUG AGACAGUUCG GUCCCUAUCC GUCGCGGGCG UU GGAAAUU UGAGAGGAGC UGUCCUUAGU ACGAGAGGAC CGGGAUGGAC UUACCGCUGG UGUACCAGUU GUUCUGCCAA GGG CAUUGC UGGGUAGCUA UGUAGGGAAG GGAUAAACGC UGAAAGCAUC UAAGUGUGAA GCCCACCUCA AGAUGAGAUU UCCC AUUUC UUUAAGAAAG UAAGACCCCU GAGAGAUGAU CAGGUAGAUA GGUUGGAAGU GGAAGGCUAG UGAUAGUUGG AGCGG ACCA AUACUAAUCG GUCGAGGACU UAAC

GENBANK: GENBANK: CP002621.1

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Macromolecule #2: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 37.433188 KDa
SequenceString:
UGUGGUGGCG AUAGCGAGAA GGAUACACCU GUUCCCAUGC CGAACACAGA AGUUAAGCUU CUUAGCGCCG AUUGUAGUGA AGGGUUUCC CUUUGUGAGA GUAGGACGUC GCCACGC

GENBANK: GENBANK: CP002621.1

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Macromolecule #3: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 22.498104 KDa
SequenceString: TKGILGKKVG MTQIFTESGE LIPVTVVEAT PNVVLQVKTV ETDGYEAIQV GYQDKREVLS NKPAKGHVAK ANTAPKRFIK EFKNVELGE YEVGKEIKVD VFQAGDVVDV TGTTKGKGFQ GAIKRHGQSR GPMSHGSRYH RRPGSMGPVA PNRVFKNKRL A GRMGGDRV ...String:
TKGILGKKVG MTQIFTESGE LIPVTVVEAT PNVVLQVKTV ETDGYEAIQV GYQDKREVLS NKPAKGHVAK ANTAPKRFIK EFKNVELGE YEVGKEIKVD VFQAGDVVDV TGTTKGKGFQ GAIKRHGQSR GPMSHGSRYH RRPGSMGPVA PNRVFKNKRL A GRMGGDRV TIQNLEVVKV DVERNVILIK GNIPGAKKSL ITIKSAVKA

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #4: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 22.384504 KDa
SequenceString: PNVALFKQDG TQNGEITLNE EIFGIEPNES VVYDAIIMQR ASLRQGTHAV KNRSAVRGGG RKPWRQKGTG RARQGSIRSP QWRGGGVVF GPTPRSYSYK LPKKVRRLAM KSVLSDKVAE NNLVAVEGLS FDAPKTKEFK QVLANLSIDT KVLVVLENGN D FAALSARN ...String:
PNVALFKQDG TQNGEITLNE EIFGIEPNES VVYDAIIMQR ASLRQGTHAV KNRSAVRGGG RKPWRQKGTG RARQGSIRSP QWRGGGVVF GPTPRSYSYK LPKKVRRLAM KSVLSDKVAE NNLVAVEGLS FDAPKTKEFK QVLANLSIDT KVLVVLENGN D FAALSARN LPNVSVVTSD NVSVLDVVSA NKVLATQTAL TQIEEVLA

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #5: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 19.863113 KDa
SequenceString:
NRLKEKYIKE VTPSLVEKFN YSSVMQTPKV DKIVINMGVG DAVSNAKNLD KAVEELALIT GQKPLITKAK KSIAGFRLRE GMPIGAKVT LRGERMYEFL DKLVTVSLPR VRDFHGVSKK AFDGRGNYTL GIKEQLIFPE VDYDLVDKVR GMDIVIVTTA N TDEESREL LAQLGMPFQ

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #6: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 19.164871 KDa
SequenceString:
SRIGNKVVVL PAGVEIKQDG NNITVKGPKG ELTREFSSDI KMNIEGNEVT FTRPNDSKEM KTIHGTTRAN FNNMVVGVSE GFQKALELI GVGYRAQVQG NKLTLNVGYS HPVEMTAPEG VTFEVPANTQ VIVKGINKEV VGELAANIRG VRPPEPYKGK G IRYVGEFV RRKEGKTG

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #7: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 16.099585 KDa
SequenceString:
MRTTYMAKAG EVERKWYVVD ATDVPLGRLS AVVASVLRGK NKPTFTPHVD TGDFVIVINA DKVKLTGKKA TDKIYYRHSM YPGGLKSVT AGELRDKNSR RLIETSVKGM LPKNTLGRKQ FTKLNVYGGA EHPHAAQQPE VLDITN

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #8: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 13.165275 KDa
SequenceString:
MIQQESRLRV ADNSGAREIL TIKVLGGSGR KTANIGDVIV ATVKQATPGG VVKKGEVVKA VIVRTKSGAR RADGSYIKFD ENAAVIIRD DKSPRGTRIF GPVARELREN NFMKIVSLAP EVL

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #9: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 15.602868 KDa
SequenceString:
MKLHELKPAE GSRQVRNRVG RGTSSGNGKT AGRGQKGQKA RSGGGVRLGF EGGQTPLFRR LPKRGFTNIN RKDYAVVNLD TLNRFEDGT EVTPVVLKEA GIVKNEKAGI KVLADGELTK KLTVKAAKFS KSAQEAIEAA GGSIEVI

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #10: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 15.960901 KDa
SequenceString:
MLVPKRVKHR REFRGKMRGE AKGGKEVAFG EWGLQATESH WITNRQIEAA RIAMTRYMKR GGKVWIKIFP HKSYTSKAIG VRMGKGKGA PEGWVSPVKR GKIMFEIAGV PEEVAREALR LASHKLPVKT KIVKREEMGG ES

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #11: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 14.156251 KDa
SequenceString:
YRKLGRTSSQ RKAMLRDITT DLIINERIVT TEARAKEVRS TVEKMITLGK RGDLHARRQA ATFVRNEVAS VREEDESIVV ESALQKLFN DLGPRFAERQ GGYTRILKTE PRRGDAAPMV VIEFV

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #12: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 12.806634 KDa
SequenceString:
ITKPDKNKTR QKRHRRVRNK ISGTAECPRL NIFRSNKNIY AQVIDDVAGV TLASASALDK EISGGTKTET AAAVGKLVAE RAAEKGIKK VVFDRGGYLY HGRVQALAEA ARENGLEF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #13: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 13.113282 KDa
SequenceString:
NPLIQELTQE QLRTDIPAFR PGDTVRVHAK VVEGTRERIQ LFEGVVIKRR GAGISETYTV RKVSNGVGVE RTFPLHTPRV AQIEVVRYG KVRRAKLYYL RALHGKAARI KEIRR

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #14: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 13.542957 KDa
SequenceString:
ARVKGGTVTR KRRKKVLKLA KGYYGSKHTL FKSAKEQVMN SYYYAFRDRR QKKRDFRKLW IARINAAARM NGLSYSKLMH GLKLAEIDI NRKMLADLAV NDAAAFTALA EQAKDALSK

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #15: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 11.166986 KDa
SequenceString:
MYAIIKTGGK QVKVEVGQAI YVEKLNVEAG EKVVFDEVIL VGGESTKVGA PTVAGATVEG TVEKHGKQKK VVTFQYKPKK HSHRKQGHR QPYTKVMIEA INA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #16: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 12.126077 KDa
SequenceString:
QITSAKATAK TVRTSPRKAR LVIDLIRGKS VADAISILKF TPNKSAGIIE KVLMSAVANA ENNFDLDVES LVVSEAFVNE GPTMKRFRP RAKGSASPIN KRTSHITVVV TEK

UniProtKB: Large ribosomal subunit protein uL22

+
Macromolecule #17: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 10.297111 KDa
SequenceString:
ELLDVIKRPV ITEKSMLAMD EKKYTFEVDT RANKTLVKQA VESAFDVKVA NVNILNVRPK FKRMGKYAGY TKKRRKAIVT LTEDSKEIQ

UniProtKB: Large ribosomal subunit protein uL23

+
Macromolecule #18: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 10.892797 KDa
SequenceString:
MFVKKGDKVK VITGKDKNKE GVVLAAFPKQ DKVIVEGVNV VKKHQKPNQA APQGGILEVE APIHVSNVMV IDPSNGEATK VAFKEVDGK KVRVSKKTGE VL

UniProtKB: Large ribosomal subunit protein uL24

+
Macromolecule #19: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 8.146118 KDa
SequenceString:
STSNGRDSES KRLGAKSADG QTVTGGSILY RQRGTKIYPG VNVGIGGDDT LFAKVDGVVR FERKGRDKKQ VSVYPV

UniProtKB: Large ribosomal subunit protein bL27

+
Macromolecule #20: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 6.072187 KDa
SequenceString:
AKVCYFTGRK TSSGNNRSHA MNSTKRTVKP NLQKVRVLID GKPKKVWVSA RALK

UniProtKB: Large ribosomal subunit protein bL28

+
Macromolecule #21: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 7.211366 KDa
SequenceString:
KVKEIRELTT AEMLDKEKQL KEELFNLRFQ LATGQLENTA RIKEVRQSIA RIKTVLREQA N

UniProtKB: Large ribosomal subunit protein uL29

+
Macromolecule #22: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 6.234273 KDa
SequenceString:
AELKITLKRS VIGRPQNQRA TVKALGLGKV NSTVTKPANE AIKGMVNTIS HLVDVEEV

UniProtKB: Large ribosomal subunit protein uL30

+
Macromolecule #23: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 6.217372 KDa
SequenceString:
AVPARRTSKA KKAKRRTHYK LTIKGLNACS NCGEMKKSHH VCPACGHYDG KDVMSK

UniProtKB: Large ribosomal subunit protein bL32

+
Macromolecule #24: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 6.052027 KDa
SequenceString:
MRVNITLECT SCKERNYLTN KNKRNNPDRL EKQKYCPRER KVTLHRETK

UniProtKB: Large ribosomal subunit protein bL33

+
Macromolecule #25: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 5.373507 KDa
SequenceString:
MKRTYQPNKR KRQKVHGFRK RMSTKNGRRV LASRRRKGRK VISA

UniProtKB: Large ribosomal subunit protein bL34

+
Macromolecule #26: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 7.466941 KDa
SequenceString:
PKQKTHRGLA KRVKRTGGGG LKRGRAFTSH RFHGKTKKQR RQLRKASMVA KGDYKRIRQQ LARM

UniProtKB: Large ribosomal subunit protein bL35

+
Macromolecule #27: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterococcus faecalis OG1RF (bacteria)
Molecular weightTheoretical: 4.440534 KDa
SequenceString:
MKVRPSVKPM CEHCKVIRRK GRVMVICPAN PKHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

+
Macromolecule #28: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 28 / Number of copies: 3 / 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

-
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
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

-
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: 2.9 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-6wu9:
50S subunit of 70S Ribosome Enterococcus faecalis MultiBody refinement

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