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- EMDB-15533: Cryo-EM structure of the proline-rich antimicrobial peptide droso... -

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Basic information

Entry
Database: EMDB / ID: EMD-15533
TitleCryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit
Map datapost masked
Sample
  • Complex: Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit
    • Protein or peptide: x 30 types
    • RNA: x 2 types
  • Ligand: x 5 types
KeywordsE.coli / Drosocin / Dro1 / antimicrobial peptide / proline-rich / PrAMP / 50S / RIBOSOME
Function / homology
Function and homology information


response to radiation / ribosomal large subunit assembly / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding ...response to radiation / ribosomal large subunit assembly / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L25, short-form / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : ...Ribosomal protein L25, short-form / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / 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 L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / 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 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 L9/RNase H1, N-terminal / 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 L2, bacterial/organellar-type / 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. / :
Similarity search - Domain/homology
Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL13 ...Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL34 / Uncharacterized protein / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL24
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli BW25113 (bacteria) / Drosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsKoller TO / Morici M / Wilson DN
Funding support Germany, 1 items
OrganizationGrant numberCountry
Other governmentDLR01Kl1820 Germany
CitationJournal: Nat Chem Biol / Year: 2023
Title: Structural basis for translation inhibition by the glycosylated drosocin peptide.
Authors: Timm O Koller / Martino Morici / Max Berger / Haaris A Safdari / Deepti S Lele / Bertrand Beckert / Kanwal J Kaur / Daniel N Wilson /
Abstract: The proline-rich antimicrobial peptide (PrAMP) drosocin is produced by Drosophila species to combat bacterial infection. Unlike many PrAMPs, drosocin is O-glycosylated at threonine 11, a post- ...The proline-rich antimicrobial peptide (PrAMP) drosocin is produced by Drosophila species to combat bacterial infection. Unlike many PrAMPs, drosocin is O-glycosylated at threonine 11, a post-translation modification that enhances its antimicrobial activity. Here we demonstrate that the O-glycosylation not only influences cellular uptake of the peptide but also interacts with its intracellular target, the ribosome. Cryogenic electron microscopy structures of glycosylated drosocin on the ribosome at 2.0-2.8-Å resolution reveal that the peptide interferes with translation termination by binding within the polypeptide exit tunnel and trapping RF1 on the ribosome, reminiscent of that reported for the PrAMP apidaecin. The glycosylation of drosocin enables multiple interactions with U2609 of the 23S rRNA, leading to conformational changes that break the canonical base pair with A752. Collectively, our study reveals novel molecular insights into the interaction of O-glycosylated drosocin with the ribosome, which provide a structural basis for future development of this class of antimicrobials.
History
DepositionAug 5, 2022-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15533.png

Downloads & links

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Map

FileDownload / File: emd_15533.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost masked
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 600 pix.
= 480. Å		0.8 Å/pix.
x 600 pix.
= 480. Å		0.8 Å/pix.
x 600 pix.
= 480. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
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Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.034172185 - 0.11462202
Average (Standard dev.)0.00009906522 (±0.0017050977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 480.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half 2

Fileemd_15533_half_map_1.map
Annotationhalf 2
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Half map: half 1

Fileemd_15533_half_map_2.map
Annotationhalf 1
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Sample components

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Entire : Cryo-EM structure of the proline-rich antimicrobial peptide droso...

EntireName: Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit
Components
  • Complex: Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit
    • 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
    • Protein or peptide: 50S ribosomal protein L31
    • Protein or peptide: Drosocin1
    • RNA: 23S ribosomal RNA
    • RNA: 5S ribosomal RNA
    • 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 L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L9
    • 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 L25
    • 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
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-alpha-D-galactopyranose
  • Ligand: MAGNESIUM ION
  • Ligand: SPERMINE
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of the proline-rich antimicrobial peptide droso...

SupramoleculeName: Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 1.5 MDa

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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 BW25113 (bacteria)
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 BW25113 (bacteria)
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 BW25113 (bacteria)
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 BW25113 (bacteria)
Molecular weightTheoretical: 4.37739 KDa
SequenceString:
MKVRASVKKL CRNCKIVKRD GVIRVICSAE PKHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #5: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 7.887117 KDa
SequenceString:
MKKDIHPKYE EITASCSCGN VMKIRSTVGH DLNLDVCSKC HPFFTGKQRD VATGGRVDRF NKRFNIPGSK

UniProtKB: Large ribosomal subunit protein bL31

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Macromolecule #6: Drosocin1

MacromoleculeName: Drosocin1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 2.204579 KDa
SequenceString:
GKPRPYSPRP TSHPRPIRV

UniProtKB: Uncharacterized protein

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Macromolecule #9: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
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 #10: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
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 #11: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
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 #12: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 20.333611 KDa
SequenceString:
MAKLHDYYKD EVVKKLMTEF NYNSVMQVPR VEKITLNMGV GEAIADKKLL DNAAADLAAI SGQKPLITKA RKSVAGFKIR QGYPIGCKV TLRGERMWEF FERLITIAVP RIRDFRGLSA KSFDGRGNYS MGVREQIIFP EIDYDKVDRV RGLDITITTT A KSDEEGRA LLAAFDFPFR K

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #13: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 18.932791 KDa
SequenceString:
MSRVAKAPVV VPAGVDVKIN GQVITIKGKN GELTRTLNDA VEVKHADNTL TFGPRDGYAD GWAQAGTARA LLNSMVIGVT EGFTKKLQL VGVGYRAAVK GNVINLSLGF SHPVDHQLPA GITAECPTQT EIVLKGADKQ VIGQVAADLR AYRRPEPYKG K GVRYADEV VRTKEAKKK

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #14: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 15.78902 KDa
SequenceString:
MQVILLDKVA NLGSLGDQVN VKAGYARNFL VPQGKAVPAT KKNIEFFEAR RAELEAKLAE VLAAANARAE KINALETVTI ASKAGDEGK LFGSIGTRDI ADAVTAAGVE VAKSEVRLPN GVLRTTGEHE VSFQVHSEVF AKVIVNVVAE

UniProtKB: Large ribosomal subunit protein bL9

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Macromolecule #15: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
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 #16: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
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 #17: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
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 #18: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 15.312269 KDa
SequenceString:
MLQPKRTKFR KMHKGRNRGL AQGTDVSFGS FGLKAVGRGR LTARQIEAAR RAMTRAVKRQ GKIWIRVFPD KPITEKPLAV RMGKGKGNV EYWVALIQPG KVLYEMDGVP EELAREAFKL AAAKLPIKTT FVTKTVM

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #19: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 14.393657 KDa
SequenceString:
MRHRKSGRQL NRNSSHRQAM FRNMAGSLVR HEIIKTTLPK AKELRRVVEP LITLAKTDSV ANRRLAFART RDNEIVAKLF NELGPRFAS RAGGYTRILK CGFRAGDNAP MAYIELVDRS EKAEAAAE

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #20: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 12.794668 KDa
SequenceString:
MDKKSARIRR ATRARRKLQE LGATRLVVHR TPRHIYAQVI APNGSEVLVA ASTVEKAIAE QLKYTGNKDA AAAVGKAVAE RALEKGIKD VSFDRSGFQY HGRVQALADA AREAGLQF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #21: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 13.159278 KDa
SequenceString:
MSNIIKQLEQ EQMKQDVPSF RPGDTVEVKV WVVEGSKKRL QAFEGVVIAI RNRGLHSAFT VRKISNGEGV ERVFQTHSPV VDSISVKRR GAVRKAKLYY LRERTGKAAR IKERLN

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #22: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 13.528024 KDa
SequenceString:
MARVKRGVIA RARHKKILKQ AKGYYGARSR VYRVAFQAVI KAGQYAYRDR RQRKRQFRQL WIARINAAAR QNGISYSKFI NGLKKASVE IDRKILADIA VFDKVAFTAL VEKAKAALA

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #23: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
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 #24: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
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 #25: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 11.22216 KDa
SequenceString:
MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKE GQNLDFVGGA E

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #26: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 11.33925 KDa
SequenceString:
MAAKIRRDDE VIVLTGKDKG KRGKVKNVLS SGKVIVEGIN LVKKHQKPVP ALNQPGGIVE KEAAIQVSNV AIFNAATGKA DRVGFRFED GKKVRFFKSN SETIK

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #27: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
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 L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 9.14654 KDa
SequenceString:
MAHKKAGGST RNGRDSEAKR LGVKRFGGES VLAGSIIVRQ RGTKFHAGAN VGCGRDHTLF AKADGKVKFE VKGPKNRKFI SIEAE

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #29: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 9.027551 KDa
SequenceString:
MSRVCQVTGK RPVTGNNRSH ALNATKRRFL PNLHSHRFWV ESEKRFVTLR VSAKGMRVID KKGIDTVLAE LRARGEKY

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #30: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 7.286464 KDa
SequenceString:
MKAKELREKS VEELNTELLN LLREQFNLRM QAASGQLQQS HLLKQVRRDV ARVKTLLNEK AGA

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #31: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 6.55482 KDa
SequenceString:
MAKTIKITQT RSAIGRLPKH KATLLGLGLR RIGHTVERED TPAIRGMINA VSFMVKVEE

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #32: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 6.463445 KDa
SequenceString:
MAVQQNKPTR SKRGMRRSHD ALTAVTSLSV DKTSGEKHLR HHITADGYYR GRKVIAK

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #7: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 941.463375 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 GGGAGCACGC UUAGGCGUGU GACUGC GUA CCUUUUGUAU AAUGGGUCAG CGACUUAUAU UCUGUAGCAA GGUUAACCGA AUAGGGGAGC CGAAGGGAAA CCGAGUC UU AACUGGGCGU UAAGUUGCAG GGUAUAGACC CGAAACCCGG UGAUCUAGCC AUGGGCAGGU UGAAGGUUGG GUAACACU A ACUGGAGGAC CGAACCGACU AAU(1MG)(PSU)(5MU)GAAA AAUUAGCGGA UGACUUGUGG CUGGGGGUGA AAGGCCA AU CAAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACU G UUUCGGCAAG GGGGUCAUCC CGACUUACCA ACCCGAUGCA AACUGCGAAU ACCGGAGAAU GUUAUCACGG GAGACACAC GGCGGG(PSU)GCU AACGUCCGUC GUGAAGAGGG AAACAACCCA GACCGCCAGC UAAGGUCCCA AAGUCAUGGU UAAGUG GGA AACGAUGUGG GAAGGCCCAG ACAGCCAGGA UGUUGGCUUA GAAGCAGCCA UCAUUUAAAG AAAGCGUAAU AGCUCAC UG GUCGAGUCGG CCUGCGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU GCGUUGUU G GGUAGGGGAG CGUUCUGUAA GCCUGCGAAG GUGUGCUGUG AGGCAUGCUG GAGGUAUCAG AAGUGCGAAU GCUGACAUA AGUAACGAUA AAGCGGGUGA AAAGCCCGCU CGCCGGAAGA CCAAGGGUUC CUGUCCAACG UUAAUCGGGG CAGGGUGAGU CGACCCCUA AGGCGAGGCC GAAAGGCGUA GUCGAUGGGA AACAGGUUAA UAUUCCUGUA CUUGGUGUUA CUGCGAAGGG G GGACGGAG AAGGCUAUGU UGGCCGGGCG ACGGUUGUCC CGGUUUAAGC GUGUAGGCUG GUUUUCCAGG CAAAUCCGGA AA AUCAAGG CUGAGGCGUG AUGACGAGGC ACUACGGUGC UGAAGCAACA AAUGCCCUGC UUCCAGGAAA AGCCUCUAAG CAU CAGGUA ACAUCAAAUC GUACCCCAAA CCGACACAGG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGA AGGAA CUAGGCAAAA UGGUGCCGUA ACUUCGGGAG AAGGCACGCU GAUAUGUAGG UGAGGUCCCU CGCGGAUGGA GCUGA AAUC AGUCGAAGAU ACCAGCUGGC UGCAACUGUU UAUUAAAAAC ACAGCACUGU GCAAACACGA AAGUGGACGU AUACGG UGU GACGCCU(2MG)CC CGGUGCCGGA AGGUUAAUUG AUGGGGUUAG CGCAAGCGAA GCUCUUGAUC GAAGCCCCGG UAA ACGGCG GCCG(PSU)AACUA (PSU)AACGGUCCU AAGGUAGCGA AA(5MU)UCCUUGU CGGGUAAGUU CCGAC(5MC)UG C ACGAAUGGCG UAAUGAUGGC CAGGCUGUCU CCACCCGAGA CUCAGUGAAA UUGAACUCGC UGUGAAGAUG CAGUGUACC CGCGGCAAGA CGGAAAGACC CCGU(G7M)AACCU UUACUAUAGC UUGACACUGA ACAUUGGACC UUGAUGUGUA GGAUAG GUG GGAGGCUUUG AAGUGUGGAC GCCAGUCUGC AUGGAGCCGA CCUUGAAAUA CCACCCUUUA AUGUUUGAUG UUCUAAC GU UGACCCCUAA UCGGGGUUGC GGACAGUGUC UGGUGGGUAG UUUGACUG(OMG)G GCGGUCUCCU CCUAAAGAGU AACG GAGGA GCACGAAGGU UGGCUAAUCC UGGUCGGACA UCAGGAGGUU AGUGCAAUGG CAUAAGCCAG CUUGACUGCG AGCGU GACG GCGCGAGCAG GUGCGAAAGC AGGUCAUAGU GAUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUCAACGGA UAAAAG GUA CUCCG(2MG)GGA(H2U) AACAGGC(PSU)GA UACCGCCCAA GAGUUCAUAU CGACGGCGGU GUUUGGCA(OMC)C U CG(2MA)(PSU)GUCG GCUCAUCACA UCCUGGGGCU GAAGUAGGUC CCAAGGGUAU GGC(OMU)GUUCGC CAUUUAAAGU GGUACGCGA GC(PSU)GGGUUUA GAACGUCGUG AGACAG(PSU)(PSU)CG GUCCCUAUCU GCCGUGGGCG CUGGAGAAC UGAGGGGGGC UGCUCCUAGU ACGAGAGGAC CGGAGUGGAC GCAUCACUGG UGUUCGGGUU GUCAUGCCAA UGGCACUGCC CGGUAGCUA AAUGCGGAAG AGAUAAGUGC UGAAAGCAUC UAAGCACGAA ACUUGCCCCG AGAUGAGUUC UCCCUGACCC U UUAAGGGU CCUGAAGGAA CGUUGAAGAC GACGACGUUG AUAGGCCGGG UGUGUAAGCG CAGCGAUGCG UUGAGCUAAC CG GUACUAA UGAACCGUGA GGCUUAACCU

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Macromolecule #8: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 8 / Number of copies: 1
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 38.79009 KDa
SequenceString:
UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCU CCCCAUGCGA GAGUAGGGAA CUGCCAGGCA U

+
Macromolecule #33: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 33 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #34: 2-acetamido-2-deoxy-alpha-D-galactopyranose

MacromoleculeName: 2-acetamido-2-deoxy-alpha-D-galactopyranose / type: ligand / ID: 34 / Number of copies: 1 / Formula: A2G
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-A2G:
2-acetamido-2-deoxy-alpha-D-galactopyranose / N-Acetylgalactosamine

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Macromolecule #35: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 35 / Number of copies: 216 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #36: SPERMINE

MacromoleculeName: SPERMINE / type: ligand / ID: 36 / Number of copies: 1 / Formula: SPM
Molecular weightTheoretical: 202.34 Da
Chemical component information

ChemComp-SPM:
SPERMINE / Spermine

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Macromolecule #37: water

MacromoleculeName: water / type: ligand / ID: 37 / Number of copies: 42 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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: 7.4
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
100.0 mMC2H3KO2Potassiumacetate
25.0 mMC4H6MgO4Magnesiumacetate
GridModel: Quantifoil R3/3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 3
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
Details8 OD260/mL

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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 / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.4 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

12573

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0) / Software - details: Beta
Final 3D classificationNumber classes: 6 / Avg.num./class: 100000 / Software - Name: RELION (ver. 4.0) / Software - details: beta
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0) / Software - details: beta
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159749
FSC plot (resolution estimation)

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