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- EMDB-52635: 50S subunit of P. gingivalis ribosome with Lefamulin -

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Basic information

Entry
Database: EMDB / ID: EMD-52635
Title50S subunit of P. gingivalis ribosome with Lefamulin
Map data50S subunit map obtained from the Multibody refinement job of RELION.
Sample
  • Complex: 50S subunit of P. gingivalis ribosome with Lefamulin
    • Protein or peptide: x 30 types
    • RNA: x 1 types
  • RNA: x 1 types
  • Ligand: x 6 types
KeywordsRibosome / antibiotics / macrolide-resistance
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / cytoplasm
Similarity search - Function
Protein of unknown function DUF4295 / Domain of unknown function (DUF4295) / : / Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L31 signature. / Ribosomal protein L31 ...Protein of unknown function DUF4295 / Domain of unknown function (DUF4295) / : / Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L2 signature. / Ribosomal protein L2, conserved site / :
Similarity search - Domain/homology
Large ribosomal subunit protein uL23 / DUF4295 domain-containing protein / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 ...Large ribosomal subunit protein uL23 / DUF4295 domain-containing protein / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL30 / 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 uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHiregange DG / Bashan A / Yonath A
Funding support1 items
OrganizationGrant numberCountry
Other privateTHE HELEN AND MILTON A. KIMMELMAN CENTER FOR BIOMOLECULAR STRUCTURE AND ASSEMBLY
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.
Authors: Disha-Gajanan Hiregange / Sarit Samiya / Danuta Mizgalska / Efrat Ben-Zeev / Miriam Waghalter / Andre Rivalta / K Shanmugha Rajan / Yehuda Halfon / Elinor Breiner-Goldstein / Igor ...Authors: Disha-Gajanan Hiregange / Sarit Samiya / Danuta Mizgalska / Efrat Ben-Zeev / Miriam Waghalter / Andre Rivalta / K Shanmugha Rajan / Yehuda Halfon / Elinor Breiner-Goldstein / Igor Kaczmarczyk / Aneta Sroka / Masato Taoka / Yuko Nobe / Toshiaki Isobe / Susanne Paukner / Ella Zimmerman / Anat Bashan / Jan Potempa / Ada Yonath /
Abstract: Porphyromonas gingivalis, an anaerobic pathogen in chronic periodontitis, belongs to the Bacteroidota phylum and is associated with various virulence factors. Its antibiotic-resistant strains and its ...Porphyromonas gingivalis, an anaerobic pathogen in chronic periodontitis, belongs to the Bacteroidota phylum and is associated with various virulence factors. Its antibiotic-resistant strains and its propensity to form biofilms pose a challenge to effective treatment. To explore therapeutic avenues, we studied the high-resolution cryogenic electron microscope structures of ribosomes from the wild-type P. gingivalis W83 and the macrolide-resistant mutant strain ermΔporN. The structural analysis revealed unique features primarily at the ribosome periphery. Together with the distinctive distribution of ribosomal RNA modifications, these findings offer insights into the therapeutical potential, such as creation of novel therapeutic compounds inhibiting the specific cellular functions of the P. gingivalis ribosomes. Moreover, the high-resolution structure of the ermΔporN ribosome in its complex with the approved antibiotic lefamulin suggests its repurposing against P. gingivalis. Furthermore, we provide a foundation for additional effective strategies to treat periodontitis and associated systemic diseases.
History
DepositionJan 28, 2025-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52635.png

Downloads & links

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Map

FileDownload / File: emd_52635.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation50S subunit map obtained from the Multibody refinement job of RELION.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 440 pix.
= 370.48 Å		0.84 Å/pix.
x 440 pix.
= 370.48 Å		0.84 Å/pix.
x 440 pix.
= 370.48 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.15341572 - 0.29371944
Average (Standard dev.)0.00028773042 (±0.0063967365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 370.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52635_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52635_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : 50S subunit of P. gingivalis ribosome with Lefamulin

EntireName: 50S subunit of P. gingivalis ribosome with Lefamulin
Components
  • Complex: 50S subunit of P. gingivalis ribosome with Lefamulin
    • Protein or peptide: Large ribosomal subunit protein bL28
    • Protein or peptide: Large ribosomal subunit protein uL29
    • Protein or peptide: Large ribosomal subunit protein uL5
    • Protein or peptide: Large ribosomal subunit protein bL31B
    • Protein or peptide: Large ribosomal subunit protein uL30
    • Protein or peptide: Large ribosomal subunit protein bL32
    • Protein or peptide: Large ribosomal subunit protein bL34
    • Protein or peptide: Large ribosomal subunit protein bL35
    • Protein or peptide: Large ribosomal subunit protein bL36
    • RNA: 23S rRNA
    • Protein or peptide: Large ribosomal subunit protein uL2
    • Protein or peptide: Large ribosomal subunit protein uL3
    • Protein or peptide: Large ribosomal subunit protein uL4
    • Protein or peptide: Large ribosomal subunit protein uL13
    • Protein or peptide: Large ribosomal subunit protein uL15
    • Protein or peptide: Large ribosomal subunit protein uL16
    • Protein or peptide: Large ribosomal subunit protein bL17
    • Protein or peptide: Large ribosomal subunit protein uL18
    • Protein or peptide: Large ribosomal subunit protein bL19
    • Protein or peptide: Large ribosomal subunit protein bL20
    • Protein or peptide: Large ribosomal subunit protein bL21
    • Protein or peptide: Large ribosomal subunit protein uL22
    • Protein or peptide: Large ribosomal subunit protein uL23
    • Protein or peptide: Large ribosomal subunit protein uL24
    • Protein or peptide: Large ribosomal subunit protein bL25
    • Protein or peptide: Large ribosomal subunit protein bL27
    • Protein or peptide: Large ribosomal subunit protein bL9
    • Protein or peptide: DUF4295 domain-containing protein
    • Protein or peptide: Large ribosomal subunit protein uL6
    • Protein or peptide: Large ribosomal subunit protein uL14
    • Protein or peptide: Large ribosomal subunit protein bL33
  • RNA: 5S rRNA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: Lefamulin
  • Ligand: POTASSIUM ION
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: 50S subunit of P. gingivalis ribosome with Lefamulin

SupramoleculeName: 50S subunit of P. gingivalis ribosome with Lefamulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10, #12-#32
Source (natural)Organism: Porphyromonas gingivalis (bacteria)

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Macromolecule #1: Large ribosomal subunit protein bL28

MacromoleculeName: Large ribosomal subunit protein bL28 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 9.027753 KDa
SequenceString:
MSKICQITGK KAMVGNNVSH SKRRTKRVFD VNLFRKKFYW VEQDCWVVLR ISAAGLRLIN KIGLDAAIKR AAEKGFLNA

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #2: Large ribosomal subunit protein uL29

MacromoleculeName: Large ribosomal subunit protein uL29 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 7.499825 KDa
SequenceString:
MKIAEIKELA TKELQERLDA EVAAYDQMRI NHAVSPLDSP AKLKHQRRMI AQMKTVLRQR ELNK

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #3: Large ribosomal subunit protein uL5

MacromoleculeName: Large ribosomal subunit protein uL5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 20.912633 KDa
SequenceString:
MSATANLKKD YQERIVPALM KQFGYTSVMQ VPVLKKIVIN QGLGMATGDK KIIDVAVSEL TAITGQKAVP TVSKKDISNF KLRKKMPIG VMVTLRREQM YEFLERLVRI ALPRIRDFKG IESKLDGRGN YTLGINEQII FPEINIDAIT KILGMNITFV T SAQSDEEG YALLKEFGLP FKNAKKQN

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #4: Large ribosomal subunit protein bL31B

MacromoleculeName: Large ribosomal subunit protein bL31B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 9.816323 KDa
SequenceString:
MKKGIHPENY RPVVFKDMSN EDIFITRSTM EAKETIEIDG VTYPLIKVEI SNTSHPFFTG KAKLVDTAGR VDKFMSRYGD RNKKK

UniProtKB: Large ribosomal subunit protein bL31B

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Macromolecule #5: Large ribosomal subunit protein uL30

MacromoleculeName: Large ribosomal subunit protein uL30 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 6.700087 KDa
SequenceString:
MAKIKIQQVR SRIRCPKDQK RTLDALGLRK LNQIVEHEAT PSILGMVNKV RHLVLIVE

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #6: Large ribosomal subunit protein bL32

MacromoleculeName: Large ribosomal subunit protein bL32 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 6.958199 KDa
SequenceString:
MAHPKRRQSK TRTAKRRTHD KAVMPTLAKC PNCGAWHIYH TVCGDCGYYR GKLAIEKEVA V

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #7: Large ribosomal subunit protein bL34

MacromoleculeName: Large ribosomal subunit protein bL34 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 5.761748 KDa
SequenceString:
MKRTYQPSNR KRLNKHGFRS RMATANGRRV LAARRAKGRA KLTVSDEFVG

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #8: Large ribosomal subunit protein bL35

MacromoleculeName: Large ribosomal subunit protein bL35 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 7.518082 KDa
SequenceString:
MPKLKTNSGA KKRFALTGTG KIKRKHAFKS HILTKKTKKQ KRNLTYFSTV HKVDENAVKQ LLCLR

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #9: Large ribosomal subunit protein bL36

MacromoleculeName: Large ribosomal subunit protein bL36 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 4.601648 KDa
SequenceString:
MKVRASVKKR TPECKIVRRK GRLYVINKKN PKYKQRQG

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #12: Large ribosomal subunit protein uL2

MacromoleculeName: Large ribosomal subunit protein uL2 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 29.778553 KDa
SequenceString: MGIRKLKPTT PGQRHKVIGA FDKITASTPE KSLVVGKKKT GGRNNTGKMT MRYIGGGHKQ KYRFIDFKRT KDGIPATVKT IEYDPNRSS RIALLYYADG AKAYIIAPDG LEVGHTVMSG SEAAPEVGNA LPLANIPVGT IIHNIELRPG QGAKMVRSAG S FAQLTSRE ...String:
MGIRKLKPTT PGQRHKVIGA FDKITASTPE KSLVVGKKKT GGRNNTGKMT MRYIGGGHKQ KYRFIDFKRT KDGIPATVKT IEYDPNRSS RIALLYYADG AKAYIIAPDG LEVGHTVMSG SEAAPEVGNA LPLANIPVGT IIHNIELRPG QGAKMVRSAG S FAQLTSRE GTYVVIKMPS GEVRRILSTC KATIGSVGNS DHALEKSGKA GRSRWLGRRP HNRGVVMNPV DHPMGGGEGR QS GGHPRSR KGLYAKGLKT RAPKKHSSKY IIERRKK

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #13: Large ribosomal subunit protein uL3

MacromoleculeName: Large ribosomal subunit protein uL3 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 21.925488 KDa
SequenceString: MPGLLGKKIG MTSVFSAEGK NLPCTVIEVG PCVVTQVKTL EKDGYSALQL GFVDAKEKHT TKPLAGHFKK ANVAPKRHLA EFKNFEGEH KLGDVLNVEF FSDADFVDVV GTSKGKGFQG VVKRHGFGGV GQATHGQHNR LRAPGAVGAC SYPAKVFKGT R MAGQMGNE ...String:
MPGLLGKKIG MTSVFSAEGK NLPCTVIEVG PCVVTQVKTL EKDGYSALQL GFVDAKEKHT TKPLAGHFKK ANVAPKRHLA EFKNFEGEH KLGDVLNVEF FSDADFVDVV GTSKGKGFQG VVKRHGFGGV GQATHGQHNR LRAPGAVGAC SYPAKVFKGT R MAGQMGNE RVTVQNLEVI KVMPEHNLLL VKGSVPGAKG SILLIEK

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #14: Large ribosomal subunit protein uL4

MacromoleculeName: Large ribosomal subunit protein uL4 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 23.247879 KDa
SequenceString: MELSVYNIKG EDTGKKVVLD DSIFAIEPND HAIYLDVKQY MANQRQGTHK AKERSELSGS TRKLIRQKGS GGARRGDINS PLLSGGARV FGPRPRNYSF KLNKKLKALA RRSALSYKAK NNEIIVVEDF NFDAPKTKAF KAISAALKVG EKKVLYVLPE V NKNVYLSA ...String:
MELSVYNIKG EDTGKKVVLD DSIFAIEPND HAIYLDVKQY MANQRQGTHK AKERSELSGS TRKLIRQKGS GGARRGDINS PLLSGGARV FGPRPRNYSF KLNKKLKALA RRSALSYKAK NNEIIVVEDF NFDAPKTKAF KAISAALKVG EKKVLYVLPE V NKNVYLSA RNLPNTNLIL ANLINTYTVL ASKNLVLTER SVAVVNELFK A

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #15: Large ribosomal subunit protein uL13

MacromoleculeName: Large ribosomal subunit protein uL13 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 17.075834 KDa
SequenceString:
MDTLSFKTIS ANKATVTKEW VIVDAEGQTL GRMCAKVAKL LRGKYKPNFT PHVDCGDNVI VINADKIVLS GNKWDGRIYL RHTGYPGGQ RQFTPRDFMN KGPEYLFRKV VKGMLPKNRL GAKIIGNLYV YAGTEHKHEA QQPRQLDINS LK

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #16: Large ribosomal subunit protein uL15

MacromoleculeName: Large ribosomal subunit protein uL15 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 15.61607 KDa
SequenceString:
MNLSSLKPAE GAVKSRKRIG RGPGSGLGGT STRGHKGAKS RSGYSKKIGF EGGQMPIQRR LPKFGFKNIN RVEYKPINLS VLQTLSEAN SLTKISVEDL IAAGLVSRNS LVKILANGTV TTALTVEAHA FSKTAEEAIV RAGGSVVKL

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #17: Large ribosomal subunit protein uL16

MacromoleculeName: Large ribosomal subunit protein uL16 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 16.344123 KDa
SequenceString:
MLQPKKTKFR RQQKGRMKGF AQRGNQLSFG SFGIKSLQSK WITGRQIEAA RIAVTRYMQR QGQVWVRIFP DKPITKKGEG VRMGKGKGA PEGFVAPITP GRIIFEVEGV PYEIAKEALR LAAQKLPVTT KFVVRHDYDI QNQNA

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #18: Large ribosomal subunit protein bL17

MacromoleculeName: Large ribosomal subunit protein bL17 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 18.074082 KDa
SequenceString:
MRHNKKFNHL GRKAAHRKAM LSNMAASLIL HKRIFTTVAK AKALRIYVEP LLTKTKEDTT HSRRIAFSYL QNKYALKELF GDVAAKIAD RPGGYTRILK TGYRLGDNAA MCFIELVDYN ENMLGEAAKK ATKTRRSRKR KSADVVVEAA PAEETPKAAE E

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #19: Large ribosomal subunit protein uL18

MacromoleculeName: Large ribosomal subunit protein uL18 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 12.560597 KDa
SequenceString:
MVTKEQRRQK IKARVRGKIS GTQEKPRLTV FRSNKQIYAQ LIDDIAGRTL ASASSLKLEM TGSKKEIAAK VGDEIAKAAT EAGISTVVF DRNGYLFHGR IKELADAARK GGLKF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #20: Large ribosomal subunit protein bL19

MacromoleculeName: Large ribosomal subunit protein bL19 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 14.120454 KDa
SequenceString:
MDFIKIVNEE FKSGKEHPKF NSGDTITVEY RIKEGNKERI QKYRGVVIRI SGHGDKKRFT VRKISDGIGV ERIFPIESPF IENITVEKY GKVRRAKLYY LRGLTGKKAR IKERRVALSS KD

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #21: Large ribosomal subunit protein bL20

MacromoleculeName: Large ribosomal subunit protein bL20 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 13.324705 KDa
SequenceString:
MPRSVNHVAS RAKRKRILKL TRGYFGARKN VWTVAKNTWE KGLTYAYRDR KSKKRNFRAL WIQRINAAAR LEGMSYSRLM GALHANGIE INRKVLADLA MNHPEAFRAI VAKVKN

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #22: Large ribosomal subunit protein bL21

MacromoleculeName: Large ribosomal subunit protein bL21 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 11.843913 KDa
SequenceString:
MYVIVDIQGQ QMKVEQGRRL FVHHIKDVES GASVEFDKVL LVDNNGAITV GSPLVEGAKV VCEVLTPLVK GDKVLIFHKK RRKGYRKLN GHRQQFTEIL VKEVVA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #23: Large ribosomal subunit protein uL22

MacromoleculeName: Large ribosomal subunit protein uL22 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 15.35775 KDa
SequenceString:
MGARKHNSAE ARKEALKQMY FAKLRNVPTS PRKMRLVADM IRGMEVNRAL GVLKFSNKEA SARVEKLLRS AVANWEEKNE RKAEEGELF VSRICVDGAS TLKRLRPAPQ GRGYRIRKRS NHVTIYVDTL NNDNN

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #24: Large ribosomal subunit protein uL23

MacromoleculeName: Large ribosomal subunit protein uL23 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 11.116101 KDa
SequenceString:
MGIIIKPIIS EKMTAVTEKM SERYGFRVSP NANKIEIKKA VEAMYNVKVE DVNTMRYDGK RKNRYTKSGL IRGKEASFKK AIVTLKKGE TIDFFSNI

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #25: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 11.627664 KDa
SequenceString:
MSKLHIKKGD TVMVISGEDK GHSGRVLEVL VKEQRAIVEG LNMIKKHAKP SAKNPQGGII SKEAPIHISN LNVVDPKTGK ATRIGRRLN ENGKLVRYAK KSGEEIK

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #26: Large ribosomal subunit protein bL25

MacromoleculeName: Large ribosomal subunit protein bL25 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 21.028605 KDa
SequenceString: MKTFQLTGTP RAEFGKKAAK AIRKEDQIPA VLYGGKGEGV NFIVSQDAVR NLIYSPEIFL VELTVEGSGS YKAILKEIQF HPVTDRIIH IDFLQVTDEK PVVMEVPVVL TGHAEGVKAG GKLSLEMRKL KVKALYSEIP EKLDIDVSDL QLGKTIQVGE L HFEGLTLM ...String:
MKTFQLTGTP RAEFGKKAAK AIRKEDQIPA VLYGGKGEGV NFIVSQDAVR NLIYSPEIFL VELTVEGSGS YKAILKEIQF HPVTDRIIH IDFLQVTDEK PVVMEVPVVL TGHAEGVKAG GKLSLEMRKL KVKALYSEIP EKLDIDVSDL QLGKTIQVGE L HFEGLTLM NAKNAVVCAV KLTRAARGAA VKKQ

UniProtKB: Large ribosomal subunit protein bL25

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Macromolecule #27: Large ribosomal subunit protein bL27

MacromoleculeName: Large ribosomal subunit protein bL27 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 9.244613 KDa
SequenceString:
MAHKKGVGSS KNGRESESKR LGVKVYGGEM AKAGNILVRQ RGTVHHPGEN VGIGKDHTLY ALKSGVVVFT RKKNDRSYVS IKTES

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #28: Large ribosomal subunit protein bL9

MacromoleculeName: Large ribosomal subunit protein bL9 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 19.356211 KDa
SequenceString:
MQVILKEDVV NLGYKDDIVT VKDGYGRNFL IPQGKAVIAS ESAKKVLAEN LRQRAHKIAQ IKKEAEEKAA SMQGISLTIK AKTSSTGTI FGSVTNIQIA EELAKKGVEV DRKIIVLKPA VKEVGNYTAV VRLHKEVTVE IPFEVVSENE TIIEAKPEGA P VPVAEEPA AEAEQAEVAA E

UniProtKB: Large ribosomal subunit protein bL9

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Macromolecule #29: DUF4295 domain-containing protein

MacromoleculeName: DUF4295 domain-containing protein / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 5.559542 KDa
SequenceString:
MAKKSVATFK KGDGRTYSKV IKMVKSPKTG AYTFQEEMVP NEAVKDFFK

UniProtKB: DUF4295 domain-containing protein

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Macromolecule #30: Large ribosomal subunit protein uL6

MacromoleculeName: Large ribosomal subunit protein uL6 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 20.389811 KDa
SequenceString:
MSRIGKLPIS IPAGVTVSHK DEIVTVKGPK GELSQYVDPR ITVVIEGGMI HLERKTDDRI ERSLHGLYRS LINNMVQGVS AGFKRELEL VGVGYRASNQ GQLLELSLGF THSIFMQLPK EVTVETKSER NKNPLIILES ADKQLLGQVC MKIRSFRKPE P YKGKGVKF VGEQIRRKSG KSAGK

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #31: Large ribosomal subunit protein uL14

MacromoleculeName: Large ribosomal subunit protein uL14 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 13.086286 KDa
SequenceString:
MIQQESRLVV ADNSGAKEAL CIRVLGGTRR RYASVGDIIV VSVKSVIPSS DIKKGAVSKA VIVRTKKEVR RPDGSYIRFD DNACVLLNA AGDIRGSRIF GPVARELRGT NMKIVSLAPE VL

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #32: Large ribosomal subunit protein bL33

MacromoleculeName: Large ribosomal subunit protein bL33 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 7.356796 KDa
SequenceString:
MAKKVKGNRV QVILECTEHK ESGMPGISRY ITTKNRKNTT QRLELKKYNP ILRRMTLHKE IK

UniProtKB: Large ribosomal subunit protein bL33

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Macromolecule #10: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 10 / Number of copies: 1
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 934.217688 KDa
SequenceString: UAAGGGCAGA CGGUGGAUGC CUAGGCUCUC GGAGGCGAAG AAGGACGUGA UAAGCUGCGA AAAGCUGCGG GAAUCGGCAC AUACGAAUU GAUCCGCAGA UAUCCGAAUG GGGCAACCCG UCAGGCCAAG GCCUGACACA UGAAUUGAUU UCAUGAGCGA A CGCGGGGA ...String:
UAAGGGCAGA CGGUGGAUGC CUAGGCUCUC GGAGGCGAAG AAGGACGUGA UAAGCUGCGA AAAGCUGCGG GAAUCGGCAC AUACGAAUU GAUCCGCAGA UAUCCGAAUG GGGCAACCCG UCAGGCCAAG GCCUGACACA UGAAUUGAUU UCAUGAGCGA A CGCGGGGA ACUGAAACAU CUCAUUACCC GUAGGAGAAG AAAACAAAAG UGAUUCCCUC AGUAGUGGCG AGCGAACGGG GA UUAGCCC AAACCGGCUU UGUUUCGGCA AAGUCGGGGU AAUAGGACUU CGACAAAAGU UUAAUGAUAG AUAUAGGAGA ACC UACUGG AAAGUAUGGC CGAAGAGCAU GAAAGCUGCG UAUCCGACAU AUCGAACAAU AGACGACGGA GCACCUGAGU AGCG CGGGA CACGAGACAU CCUGUGUGAA UUGGCGGGGC CCAUCCCGUA AGGCUAAAUA CUCCCGAGAG ACCGAUAGUG AACCA GUAC CGUGAGGGAA AGGUGAAAAG AACCUCGAAC AGAGGAGUGC AAUAGACCCU GAACCCGUCU GCCUACAAGC GGUAGG AGC GCCAUUAAGG UGUGACUGCG UGCCUUUUGC AUAAUGAACC UACGAGUUAC UGUUUGUGGC AAGGUUAAUU GUUAUAA UC AAGACAAGGA GCCGAAGCGA AAGCGAGUCU UAAAAGGGCG CCCAUUUAGU CACGAGCAGU AGACGCGAAA CCAAGUGA U CUACCCUUGG UCAGGUUGAA GGUUAGGUAA CACUAACUGG AGGACCGAAU CGGUAAGCG(H2U) UGAAAAGCUU UCGAA UGAA CUGAGGGUAG GGGUGAAAGG CUAAUCAAAC UUGGAGAUAG CUCGUACUCC CCGAAAUGCA UUUAGGUGCA GCCUG (H2U)UGG AUGUUAUCAU GAGGUAGAGC GACUGAUUGG AUGCGAGGGU UUCACCGCCU AUCAAGUCCA GAUAAACUCC GA AUGCAUG AUAAUUGACC GAUGGAGUGA GGGCAUGGGU GCUAAGGUCC AUGUCCGAGA GGAGAAGAAU CCGGACCACC GGC UAAGGU CCCGAAAUAA UUGCUAAGUU GUAAAAACGA AGUCAAGAAG CAGAGACAGC UAGGAUGUUG GCUUGGAAGC AGCC AUUCA UUUAAAGAGU GCGUAACAGC UCACUAGUCG AGGAUUUUGG CAUGGAUAAU ACACGGGCAU AAGCAAUUUA CCGAA GCCG UGGGAUAUAG UUAAUAUAUC GGUAGGGGAG CAUUCCAGCG ACGUAGAAGG GAAAAGGGCG ACUUUUUCUG GAGUUU CUG GAAAAGCAAA UGUAGGUAUA AGUAACGAUA AAGGGGGCGA GAACCCCCCU CGCCGAAAGA CCAAGGUUUC CUGAUCA AC GCUAAUCGGA UCAGGGUUAG UCGGGGCCUA AGGAUAAGCC GAAUGGCGAU UCCGAUGGAA GAACCGGUUA AUAUUCCG G UACUGAUACU AGAGGCGAUG UGGUGACGGA GAAGUGACAG UCCGGCCGUC UGACGGAUUA GGCGGUUAAA GGGUGUAGA UGUUAUUCGG GGUAGGCAAA UCCGCCCUCA GAGUGCAACC UGACAGUACC GGAGUACAAG UACGAAGGGA UAAAGGACGU AACCCGGCU CCCAAGAAAA CCCGCUAAGA UAUUUCUUGU GUUACCCGUA CCGUAAACCG ACACAGGUGG UUGGGUUGAG U AUACUAAG GCGCUCGAGA GAUUCGCGGU UAAGGAACUA GGCAAAAUGG UCCUGUAACU UCGGGAGAAA GGACGCCUGU CC CGGGACA GGCCGCAGAA ACCAGGCCCA GGCGACUGUU UAACAAAAAC ACAAGGCUAU GCAAAAAAGC AAUUUGAGGU AUA UAGUCU GACACCUGCC CGGUGCUGGA AGGUUAAGAG GAGGAGUCAU GUCAAGGAGA AGCUCUGAAU UGAAGCCCCA GUAA ACGGC GCCGUAACUA UAACGGUCC(5MC) UAAGGUAGCG AAA(5MU)UCCUUG UCGGGUAAGU UCCGAC(5MC)UGC ACG AAUGGU GUAACGAUCU GGGCACUGUC UCAACCGCGA UCUCGGUGAA AUUGUAGUAU CGGUGAAGAU GCCGAUUACC CGCA ACGGG ACG(6MA)(MA6)(6MA)AGAC CCCGUGAACC UUUACUAUAG CUUUACAUUG UAUUGGGCAU CAGAUGUGUA GGA UAGGCC GGAGGCAGAG AAGCGGGUAC GCCAGUAUUC GUGGAGUCGA UGUUGAAAUA CGGCCCUUUU GAUGUUUGGG AUAC UAACU CGCGGGUGGC GAGGACAGUG UAUGGUGGGU AGUUUGACUG (OMG)GGUGGUCGC CUCCAAAAGC GUAACGGAGG C UUCUAAAG GUACCCUCAG GCCGAUUGUA AACCGGUCGC AGAGUGUAAU GGCACAAGGG UGCUUGACUG GGAGACAAAC AA GUCGCAC AGGUAGGAAA CUAGAGCAUA GUGAUCCGGU GGUCCCGCAU GGAAGGGCCA UCGCUCAAAG GAUAAAAGGU ACU CCG(2MG)GG A(OMU)AACAGGCU GAUCACUCCC AAGAGUCCAU AUCGACGGAG UGGUUUGGCA CCU(5OC)G(2MA)UG U CGGCUCGUCA CAUCCUGGGG CUGGAGAAGG UCCCAAGGGU UGGGCU(OMG)UUC GCCCAUUAAA GUGGCACGCG AGC (PSU)GGGUU CAGAACGUCG UGAGACAGU(PSU) CGGUCUCUAU CUG(H2U)UGUGGG CGCAGGAAAU UUGCGAGGGU CU GACACUA GUACGAGAGG ACCGUG(H2U)UGG ACAGACCCCU GGUUUACCGG UUGUACCGCC AGGUGCACCG CCGGGUAUC CACGUCUGGU AAGGAUAAGU GCUGAAAGCA UCUAAGCACG AAGCCGGCCU CAAGAUAAGA UUUCCAUAAA UAGGGUGGUU AAAGACUAU GACCUUGAUA GGCUGCAGGU GUAUGAUUGG UAACAAUUAA GCCGAGCAGU ACUAAUAGCC CGAACUUU

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Macromolecule #11: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 11 / Number of copies: 1
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 35.186926 KDa
SequenceString:
UCAGGUGGUU AUAACGUUGG GGAUCCACCU CUUCCCAUUC CGAACAGAGA AGUUAAGCCC AACGGUGCCG AUGGUACUGC GUCACAGUG GGAGAGUAGG ACGCCGCCGA

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Macromolecule #33: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 33 / Number of copies: 139 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #34: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 34 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #35: Lefamulin

MacromoleculeName: Lefamulin / type: ligand / ID: 35 / Number of copies: 1 / Formula: 62B
Molecular weightTheoretical: 507.726 Da
Chemical component information

ChemComp-62B:
Lefamulin / medication, antibiotic*YM

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Macromolecule #36: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 36 / Number of copies: 18 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #37: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 37 / Number of copies: 15
Molecular weightTheoretical: 22.99 Da

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Macromolecule #38: water

MacromoleculeName: water / type: ligand / ID: 38 / Number of copies: 1380 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 223396
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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