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- EMDB-46632: E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (... -

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Basic information

Entry
Database: EMDB / ID: EMD-46632
TitleE. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)
Map data
Sample
  • Complex: E. coli 70S ribosome in complex with PrAMP rumicidin-2
    • Protein or peptide: x 29 types
    • RNA: x 2 types
  • Ligand: x 5 types
KeywordsProline-rich antimicrobial peptides / PrAMP / Ribosome / Cryo-EM
Function / homology
Function and homology information


DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / ribosome assembly / cytosolic ribosome assembly / response to radiation / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly ...DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / ribosome assembly / cytosolic ribosome assembly / response to radiation / 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 / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L25, short-form / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type ...Ribosomal protein L25, short-form / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / 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 L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein L5, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 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 L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / : / L28p-like / 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 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 L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L13 signature. / Ribosomal protein L2, domain 3 / Ribosomal protein L13, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain
Similarity search - Domain/homology
Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL3 ...Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL19
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Beatragus hunteri (mammal)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.95 Å
AuthorsPichkur EB / Panteleev PV / Konevega AL
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Rumicidins are a family of mammalian host-defense peptides plugging the 70S ribosome exit tunnel.
Authors: Pavel V Panteleev / Eugene B Pichkur / Roman N Kruglikov / Alena Paleskava / Olga V Shulenina / Ilia A Bolosov / Ivan V Bogdanov / Victoria N Safronova / Sergey V Balandin / Valeriya I ...Authors: Pavel V Panteleev / Eugene B Pichkur / Roman N Kruglikov / Alena Paleskava / Olga V Shulenina / Ilia A Bolosov / Ivan V Bogdanov / Victoria N Safronova / Sergey V Balandin / Valeriya I Marina / Tatiana I Kombarova / Olga V Korobova / Olga V Shamova / Alexander G Myasnikov / Alexander I Borzilov / Ilya A Osterman / Petr V Sergiev / Alexey A Bogdanov / Olga A Dontsova / Andrey L Konevega / Tatiana V Ovchinnikova /
Abstract: The antimicrobial resistance crisis along with challenges of antimicrobial discovery revealed the vital necessity to develop new antibiotics. Many of the animal proline-rich antimicrobial peptides ...The antimicrobial resistance crisis along with challenges of antimicrobial discovery revealed the vital necessity to develop new antibiotics. Many of the animal proline-rich antimicrobial peptides (PrAMPs) inhibit the process of bacterial translation. Genome projects allowed to identify immune-related genes encoding animal host defense peptides. Here, using genome mining approach, we discovered a family of proline-rich cathelicidins, named rumicidins. The genes encoding these peptides are widespread among ruminant mammals. Biochemical studies indicated that rumicidins effectively inhibited the elongation stage of bacterial translation. The cryo-EM structure of the Escherichia coli 70S ribosome in complex with one of the representatives of the family revealed that the binding site of rumicidins span the ribosomal A-site cleft and the nascent peptide exit tunnel interacting with its constriction point by the conservative Trp23-Phe24 dyad. Bacterial resistance to rumicidins is mediated by knockout of the SbmA transporter or modification of the MacAB-TolC efflux pump. A wide spectrum of antibacterial activity, a high efficacy in the animal infection model, and lack of adverse effects towards human cells in vitro make rumicidins promising molecular scaffolds for development of ribosome-targeting antibiotics.
History
DepositionAug 19, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46632.png

Downloads & links

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Map

FileDownload / File: emd_46632.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 441.856 Å		0.86 Å/pix.
x 512 pix.
= 441.856 Å		0.86 Å/pix.
x 512 pix.
= 441.856 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.863 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-0.6738536 - 6.2402387
Average (Standard dev.)-0.0060214223 (±0.27447963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 441.856 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46632_msk_1.map
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Additional map: #1

Fileemd_46632_additional_1.map
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Half map: #1

Fileemd_46632_half_map_1.map
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Half map: #2

Fileemd_46632_half_map_2.map
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Sample components

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Entire : E. coli 70S ribosome in complex with PrAMP rumicidin-2

EntireName: E. coli 70S ribosome in complex with PrAMP rumicidin-2
Components
  • Complex: E. coli 70S ribosome in complex with PrAMP rumicidin-2
    • 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
    • RNA: 23S rRNA
    • RNA: 5S rRNA
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: Large ribosomal subunit protein uL23
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: Large ribosomal subunit protein uL6
    • Protein or peptide: 50S ribosomal protein L9
    • Protein or peptide: Large ribosomal subunit protein uL13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: Large ribosomal subunit protein bL20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: Large ribosomal subunit protein uL24
    • Protein or peptide: Large ribosomal subunit protein bL25
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: Large ribosomal subunit protein uL29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: Rumicidin-2 (12-27)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol
  • Ligand: water

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Supramolecule #1: E. coli 70S ribosome in complex with PrAMP rumicidin-2

SupramoleculeName: E. coli 70S ribosome in complex with PrAMP rumicidin-2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#31
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.388631 KDa
SequenceString:
MAKGIREKIK LVSSAGTGHF YTTTKNKRTK PEKLELKKFD PVVRQHVIYK EAKIK

UniProtKB: Large ribosomal subunit protein bL33

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Macromolecule #2: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 5.397463 KDa
SequenceString:
MKRTFQPSVL KRNRSHGFRA RMATKNGRQV LARRRAKGRA RLTVSK

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #3: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 7.313032 KDa
SequenceString:
MPKIKTVRGA AKRFKKTGKG GFKHKHANLR HILTKKATKR KRHLRPKAMV SKGDLGLVIA CLPYA

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #4: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 4.37739 KDa
SequenceString:
MKVRASVKKL CRNCKIVKRD GVIRVICSAE PKHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #7: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 29.923619 KDa
SequenceString: MAVVKCKPTS PGRRHVVKVV NPELHKGKPF APLLEKNSKS GGRNNNGRIT TRHIGGGHKQ AYRIVDFKRN KDGIPAVVER LEYDPNRSA NIALVLYKDG ERRYILAPKG LKAGDQIQSG VDAAIKPGNT LPMRNIPVGS TVHNVEMKPG KGGQLARSAG T YVQIVARD ...String:
MAVVKCKPTS PGRRHVVKVV NPELHKGKPF APLLEKNSKS GGRNNNGRIT TRHIGGGHKQ AYRIVDFKRN KDGIPAVVER LEYDPNRSA NIALVLYKDG ERRYILAPKG LKAGDQIQSG VDAAIKPGNT LPMRNIPVGS TVHNVEMKPG KGGQLARSAG T YVQIVARD GAYVTLRLRS GEMRKVEADC RATLGEVGNA EHMLRVLGKA GAARWRGVRP TVRGTAMNPV DHPHGGGEGR NF GKHPVTP WGVQTKGKKT RSNKRTDKFI VRRRSK

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #8: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 22.291562 KDa
SequenceString: MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN (MEQ)TPGKVF KG KKMAGQMGNE ...String:
MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN (MEQ)TPGKVF KG KKMAGQMGNE RVTVQSLDVV RVDAERNLLL VKGAVPGATG SDLIVKPAVK A

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #9: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 22.121566 KDa
SequenceString: MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD ...String:
MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD VRDATGIDPV SLIAFDKVVM TADAVKQVEE MLA

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #10: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.008471 KDa
SequenceString:
MRLNTLSPAE GSKKAGKRLG RGIGSGLGKT GGRGHKGQKS RSGGGVRRGF EGGQMPLYRR LPKFGFTSRK AAITAEIRLS DLAKVEGGV VDLNTLKAAN IIGIQIEFAK VILAGEVTTP VTVRGLRVTK GARAAIEAAG GKIEE

UniProtKB: Large ribosomal subunit protein uL15

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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: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.505746 KDa
SequenceString:
MRHRKSGRQL NRNSSHRQAM FRNMAGSLVR HEIIKTTLPK AKELRRVVEP LITLAKTDSV ANRRLAFART RDNEIVAKLF NELGPRFAS RAGGYTRILK CGFRAGDNAP MAYIELVDR

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Macromolecule #12: Large ribosomal subunit protein uL23

MacromoleculeName: Large ribosomal subunit protein uL23 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.546472 KDa
SequenceString:
MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKE GQNL

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #13: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.419629 KDa
SequenceString:
GSTRNGRDSE AKRLGVKRFG GESVLAGSII VRQRGTKFHA GANVGCGRDH TLFAKADGKV KFEVKGPKNR KFISIEAE

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Macromolecule #14: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.332249 KDa
SequenceString:
AVQQNKPTRS KRGMRRSHDA LTAVTSLSVD KTSGEKHLRH HITADGYYRG RKVIAK

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #15: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.073234 KDa
SequenceString:
AKLHDYYKDE VVKKLMTEFN YNSVMQVPRV EKITLNMGVG EAIADKKLLD NAAADLAAIS GQKPLITKAR KSVAGFKIRQ GYPIGCKVT LRGERMWEFF ERLITIAVPR IRDFRGLSAK SFDGRGNYSM GVREQIIFPE IDYDKVDRVR GLDITITTTA K SDEEGRAL LAAFDFPFR

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #16: Large ribosomal subunit protein uL6

MacromoleculeName: Large ribosomal subunit protein uL6 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.801598 KDa
SequenceString:
SRVAKAPVVV PAGVDVKING QVITIKGKNG ELTRTLNDAV EVKHADNTLT FGPRDGYADG WAQAGTARAL LNSMVIGVTE GFTKKLQLV GVGYRAAVKG NVINLSLGFS HPVDHQLPAG ITAECPTQTE IVLKGADKQV IGQVAADLRA YRRPEPYKGK G VRYADEVV RTKEAKKK

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #17: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 4.028719 KDa
SequenceString:
MQVILLDKVA NLGSLGDQVN VKAGYARNFL VPQGKAVP

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Macromolecule #18: Large ribosomal subunit protein uL13

MacromoleculeName: Large ribosomal subunit protein uL13 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.050606 KDa
SequenceString:
MKTFTAKPET VKRDWYVVDA TGKTLGRLAT ELARRLRGKH KAEYTPHVDT GDYIIVLNAD KVAVTGNKRT DKVYYHHTGH IGGIKQATF EEMIARRPER VIEIAVKGML PKGPLGRAMF RKLKVYAGNE HNHAAQQPQV LDI

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #19: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.565067 KDa
SequenceString:
MIQEQTMLNV ADNSGARRVM CIKVLGGSHR RYAGVGDIIK ITIKEAIPRG KVKKGDVLKA VVVRTKKGVR RPDGSVIRFD GNACVLLNN NSEQPIGTRI FGPVTRELRS EKFMKIISLA PEVL

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #20: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.196062 KDa
SequenceString:
MLQPKRTKFR KMHKGRNRGL AQGTDVSFGS FGLKAVGRGR LTARQIEAAR RAMTRAVKRQ GKIWIRVFPD KPITEKPLAV (4D4)GKGKGNVE YWVALIQPGK VLYEMDGVPE ELAREAFKLA AAKLPIKTTF VTKTVM

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Macromolecule #21: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.663471 KDa
SequenceString:
DKKSARIRRA TRARRKLQEL GATRLVVHRT PRHIYAQVIA PNGSEVLVAA STVEKAIAEQ LKYTGNKDAA AAVGKAVAER ALEKGIKDV SFDRSGFQYH GRVQALADAA REAGLQF

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Macromolecule #22: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.028082 KDa
SequenceString:
SNIIKQLEQE QMKQDVPSFR PGDTVEVKVW VVEGSKKRLQ AFEGVVIAIR NRGLHSAFTV RKISNGEGVE RVFQTHSPVV DSISVKRRG AVRKAKLYYL RERTGKAARI KERLN

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #23: Large ribosomal subunit protein bL20

MacromoleculeName: Large ribosomal subunit protein bL20 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.396828 KDa
SequenceString:
ARVKRGVIAR ARHKKILKQA KGYYGARSRV YRVAFQAVIK AGQYAYRDRR QRKRQFRQLW IARINAAARQ NGISYSKFIN GLKKASVEI DRKILADIAV FDKVAFTALV EKAKAALA

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #24: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.586374 KDa
SequenceString:
MYAVFQSGGK QHRVSEGQTV RLEKLDIATG ETVEFAEVLM IANGEEVKIG VPFVDGGVIK AEVVAHGRGE KVKIVKFRRR KHYRKQQGH RQWFTDVKIT GISA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #25: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.253359 KDa
SequenceString:
METIAKHRHA RSSAQKVRLV ADLIRGKKVS QALDILTYTN KKAAVLVKKV LESAIANAEH NDGADIDDLK VTKIFVDEGP SMKRIMPRA KGRADRILKR TSHITVVVSD R

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #26: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.078874 KDa
SequenceString:
AAKIRRDDEV IVLTGKDKGK RGKVKNVLSS GKVIVEGINL VKKHQKPVPA LNQPGGIVEK EAAIQVSNVA IFNAATGKAD RVGFRFEDG KKVRFFKSNS ETI

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #27: Large ribosomal subunit protein bL25

MacromoleculeName: Large ribosomal subunit protein bL25 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.713465 KDa
SequenceString:
MFTINAEVRK EQGKGASRRL RAANKFPAII YGGKEAPLAI ELDHDKVMNM QAKAEFYSEV LTIVVDGKEI KVKAQDVQRH PYKPKLQHI DFVRA

UniProtKB: Large ribosomal subunit protein bL25

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Macromolecule #28: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.896354 KDa
SequenceString:
SRVCQVTGKR PVTGNNRSHA LNATKRRFLP NLHSHRFWVE SEKRFVTLRV SAKGMRVIDK KGIDTVLAEL RARGEKY

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #29: Large ribosomal subunit protein uL29

MacromoleculeName: Large ribosomal subunit protein uL29 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 7.155267 KDa
SequenceString:
KAKELREKSV EELNTELLNL LREQFNLRMQ AASGQLQQSH LLKQVRRDVA RVKTLLNEKA GA

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #30: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.423625 KDa
SequenceString:
AKTIKITQTR SAIGRLPKHK ATLLGLGLRR IGHTVEREDT PAIRGMINAV SFMVKVEE

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #31: Rumicidin-2 (12-27)

MacromoleculeName: Rumicidin-2 (12-27) / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Beatragus hunteri (mammal)
Molecular weightTheoretical: 2.008397 KDa
SequenceString:
PPHRPRPRPL PWFPPR

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Macromolecule #5: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 885.0645 KDa
SequenceString: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG ...String:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG GUUAAUGAGG CGAACCGGGG GAACUGAAAC AUCUAAGUAC CCCGAGGAAA AGAAAUCAAC CGAGAUUCCC CC AGUAGCG GCGAGCGAAC GGGGAGCAGC CCAGAGCCUG AAUCAGUGUG UGUGUUAGUG GAAGCGUCUG GAAAGGCGCG CGA UACAGG GUGACAGCCC CGUACACAAA AAUGCACAUG CUGUGAGCUC GAUGAGUAGG GCGGGACACG UGGUAUCCUG UCUG AAUAU GGGGGGACCA UCCUCCAAGG CUAAAUACUC CUGACUGACC GAUAGUGAAC CAGUACCGUG AGGGAAAGGC GAAAA GAAC CCCGGCGAGG GGAGUGAAAA AGAACCUGAA ACCGUGUACG UACAAGCAGU GGGAGCACAG CUGUGUGACU GCGUAC CUU UUGUAUAAUG GGUCAGCGAC UUAUAUUCUG UAGCAAGGUU AACCGAAUAG GGGAGCCGAA GGGAAACCGA GUCUUAA CU GGGCGUUAAG UUGCAGGGUA UAGACCCGAA ACCCGGUGAU CUAGCCAUGG GCAGGUUGAA GGUUGGGUAA CACUAACU G GAGGACCGAA CCGACUAAU(1MG) (PSU)(5MU)GAAAAAUU AGCGGAUGAC UUGUGGCUGG GGGUGAAAGG CCAAUCA AA CCGGGAGAUA GCUGGUUCUC CCCGAAAGCU AUUUAGGUAG CGCCUCGUGA AUUCAUCUCC GGGGGUAGAG CACUGUUU C GGCAAAACCC GAUGCAAACU GCGAAUACCG GAGAAUGUUA UCACGGGAGA CACACGGCGG G(PSU)GCUAACGU CCGUC GUGA AGAGGGAAAC AACCCAGACC GCCAGCUAAG GUCCCAAAGU CAUGGUUAAG UGGGAAACGA UGUGGGAAGG CCCAGA CAG CGUCGAGUCG GCCUGCGCGG AAGAUGUAAC GGGGCUAAAC CAUGCACCGA AGCUGCGGCA GCGACGCGCG UUGUUGG GU AGGGGAGCGU UCUGUAAGCC UGUGAAGGUG UGCUGUGAGG CAUGCUGGAG GUAUCAGAAG UGCGAAUGCU GACAUAAG U AACGAUAAAG CGGGUGAAAA GCCCGCUCGC CGGAAGACCA AGGGUUCCUG UCCAACGUUA AUCGGGGCAG GGUGAGUCG ACCCCUAAGG CGAGGCCGAA AGGCGUAGUC GAUGGGAAAC AGGUUAAUAU UCCUGUACUU GGUGUUACUG CGAAGGGGGG ACGGAGAAG GCUAUGUUGG CCGGGCGACG GUUGUCCCGG UUUAAGCGUG UAGGCUGGUU UUCCAGGCAA AUCCGGAAAA U CAAGGCUG AGGCGUGAUG ACGAGGCACU ACGGUGCUGA AGCAACAAAU GCCCUGCUUC CAGGAAAAGC CUCUAAGCAU CA GGUAACA UCAAAUCGUA CCCCAAACCG ACAC(6MZ)GGUGG UCAGGUAGAG AAUACCAAGG CGCUUGAGAG AACUCGGGU GAAGGAACUA GGCAAAAUGG UGCCGUAACU UCGGGAGAAG GCACGCUGAU AUGUAGGUGA GGUCCCUCGC GGAUGGAGCU GAAAUCAGU CGAAGAUACC AGCUGGCUGC AACUGUUUAU UAAAAACACA GCACUGUGCA AACACGAAAG UGGACGUAUA C GGUGUGAC GCCU(2MG)CCCGG UGCCGGAAGG UUAAUUGAUG GGGUUAGCGG CGCGAAGCUC UUGAUCGAAG CCCCGGUA A ACGGCGGCCG (PSU)AAC(3TD)A(PSU)AAC GGUCCUAAGG UAGCGAAA(5MU)U CCUUGUCGGG UAAGUUCCGA C (5MC)UGCACGA AUGGCGUAAU GAUGGCCAGG CUGUCUCCAC CCGAGACUCA GUGAAAUUGA ACUCGCUGUG (6MZ)AGA UGCAG UGUACCCGCG GCAAGACGGA AAGACCCCGU (G7M)AACCUUUAC UAUAGCUUGA CACUGAACAU AUGUUCUAAC G UUGGCCCG UGAUCCGGGU UGCGGACAGU GUCUGGUGGG UAGUUUGACU G(OMG)GGCGGUCU CCUCCUAAAG AGUAACGG A GGAGCACGAA GGUUGGCUAA UCCUGGUCGG ACAUCAGGAG GUUAGUGCAA UGGCAUAAGC CAGCUUGACU GCGAGCGUG ACGGCGCGAG CAGGUGCGAA AGCAGGUCAU AGUGAUCCGG UGGUUCUGAA UGGAAGGGCC AUCGCUCAAC GGAUAAAAGG UACUCCG(2MG)G GA(H2U)AACAGGC (PSU)GAUACCGCC CAAGAGUUCA UAUCGACGGC GGUGUUUGGC A(OMC)CUC G(2MA)(PSU)G UCGGCUCAUC ACAUCCUGGG GCUGAAGUAG GUCCCAAGGG UAUGGC(OMU)GUU CGCCAUUUAA AGUG GUACG CGAGC(PSU)GGGU UUAGAACGUC GUGAGACAG(PSU) (PSU)CGGUCCCUA UCUGCCGUGG GCGCUGGAGA ACU GAGGGG GGCUGCUCCU AGUACGAGAG GACCGGAGUG GACGCAUCAC UGGUGUUCGG GUUGUCAUGC CAAUGGCACU GCCC GGUAG CUAAAUGCGG AAGAGAUAAG UGCUGAAAGC AUCUAAGCAC GAAACUUGCC CCGAGAUGAG UUCUCCCUGA CUCCU UGAG AGUCCUGAAG GAACGUUGAA GACGACGACG UUGAUAGGCC GGGUGUGUAA GCGCAGCGAU GCGUUGAGCU AACCGG UAC UAAUGAACCG UGAGGCUUAA CCU

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Macromolecule #6: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 38.483926 KDa
SequenceString:
UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCU CCCCAUGCGA GAGUAGGGAA CUGCCAGGCA

GENBANK: GENBANK: CP049050.1

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Macromolecule #32: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 32 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #33: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 33 / Number of copies: 204 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #34: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 34 / Number of copies: 93 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #35: (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol

MacromoleculeName: (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol / type: ligand / ID: 35 / Number of copies: 1 / Formula: MS6
Molecular weightTheoretical: 151.293 Da
Chemical component information

ChemComp-MS6:
(2S)-2-amino-4-(methylsulfanyl)butane-1-thiol

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Macromolecule #36: water

MacromoleculeName: water / type: ligand / ID: 36 / Number of copies: 4308 / 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 R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 12 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 20.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 371000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

8b0x


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: OTHER
Output model

PDB-9d89:
E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)

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