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- PDB-8am9: Cryo-EM structure of the proline-rich antimicrobial peptide droso... -

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Basic information

Entry
Database: PDB / ID: 8am9
TitleCryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the elongating ribosome
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Drosocin1
  • Initiator tRNA
  • Leucine tRNA
  • mRNAMessenger RNA
KeywordsRIBOSOME / E.coli / 70S / Drosocin / Dro1 / antimicrobial peptide / proline-rich / PrAMP / Initiator tRNA / Elongation / Leucine tRNA
Function / homology
Function and homology information


ornithine decarboxylase inhibitor activity / four-way junction DNA binding / DNA endonuclease activity / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit ...ornithine decarboxylase inhibitor activity / four-way junction DNA binding / DNA endonuclease activity / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 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 / mRNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein S21 / 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 S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / 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 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27
Similarity search - Domain/homology
: / 2-acetamido-2-deoxy-alpha-D-galactopyranose / SPERMINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 ...: / 2-acetamido-2-deoxy-alpha-D-galactopyranose / SPERMINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL17 / 50S ribosomal protein L33 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein uL2 / : / : / Small ribosomal subunit protein uS8 / 30S ribosomal protein S10 / Small ribosomal subunit protein uS9 / 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 uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL24
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Escherichia coli BW25113 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKoller, T.O. / Morici, M. / Wilson, D.N.
Funding support Germany, 1items
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 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 50S ribosomal protein L33
1: 50S ribosomal protein L34
2: 50S ribosomal protein L35
3: 50S ribosomal protein L36
4: 50S ribosomal protein L31
B: 16S ribosomal RNA
C: 30S ribosomal protein S2
D: 30S ribosomal protein S3
E: 30S ribosomal protein S4
F: 30S ribosomal protein S5
G: 30S ribosomal protein S6, fully modified isoform
H: 30S ribosomal protein S7
I: 30S ribosomal protein S8
J: 30S ribosomal protein S9
K: 30S ribosomal protein S10
L: 30S ribosomal protein S11
M: 30S ribosomal protein S12
N: 30S ribosomal protein S13
O: 30S ribosomal protein S14
P: 30S ribosomal protein S15
Q: 30S ribosomal protein S16
R: 30S ribosomal protein S17
S: 30S ribosomal protein S18
T: 30S ribosomal protein S19
U: 30S ribosomal protein S20
V: 30S ribosomal protein S21
a: 23S ribosomal RNA
b: 5S ribosomal RNA
c: 50S ribosomal protein L2
d: 50S ribosomal protein L3
e: 50S ribosomal protein L4
f: 50S ribosomal protein L5
g: 50S ribosomal protein L6
h: 50S ribosomal protein L9
i: 50S ribosomal protein L13
j: 50S ribosomal protein L14
k: 50S ribosomal protein L15
l: 50S ribosomal protein L16
m: 50S ribosomal protein L17
n: 50S ribosomal protein L18
o: 50S ribosomal protein L19
p: 50S ribosomal protein L20
q: 50S ribosomal protein L21
r: 50S ribosomal protein L22
s: 50S ribosomal protein L23
t: 50S ribosomal protein L24
u: 50S ribosomal protein L25
v: 50S ribosomal protein L27
w: 50S ribosomal protein L28
x: 50S ribosomal protein L29
y: 50S ribosomal protein L30
z: 50S ribosomal protein L32
X: mRNA
Y: Initiator tRNA
8: Leucine tRNA
A: Drosocin1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,203,313353
Polymers2,195,63856
Non-polymers7,676297
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 29 types, 29 molecules 01234cdefghijklmnopqrstuvwxyz

#1: Protein 50S ribosomal protein L33 /


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A2D0APZ6
#2: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A8X6EVB8
#3: Protein 50S ribosomal protein L35 /


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A8S0FT45
#4: Protein/peptide 50S ribosomal protein L36 /


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A2X1PTA3
#5: Protein 50S ribosomal protein L31 /


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SIV2
#29: Protein 50S ribosomal protein L2 /


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A7L6YWH1
#30: Protein 50S ribosomal protein L3 /


Mass: 22291.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SQU2
#31: Protein 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: D8A1N0
#32: Protein 50S ribosomal protein L5 /


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Strain: K-12 / References: UniProt: D6IEK6
#33: Protein 50S ribosomal protein L6 /


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SR17
#34: Protein 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SFP2
#35: Protein 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / Strain: K-12 / References: UniProt: A0A656YGQ7
#36: Protein 50S ribosomal protein L14 /


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SQZ2
#37: Protein 50S ribosomal protein L15 / / Large ribosomal subunit protein uL15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02413
#38: Protein 50S ribosomal protein L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A0H3EMH6
#39: Protein 50S ribosomal protein L17 /


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A1X3JBW6
#40: Protein 50S ribosomal protein L18 /


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A514EKV0
#41: Protein 50S ribosomal protein L19 /


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A370V6W8
#42: Protein 50S ribosomal protein L20 /


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A378BCJ4
#43: Protein 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A0E2L2H1
#44: Protein 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A0F6B7N1
#45: Protein 50S ribosomal protein L23 /


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: D7Y3D8
#46: Protein 50S ribosomal protein L24 /


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: S1E9P3
#47: Protein 50S ribosomal protein L25 / / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P68919
#48: Protein 50S ribosomal protein L27 /


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SSG7
#49: Protein 50S ribosomal protein L28 /


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SME2
#50: Protein 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SQY2
#51: Protein 50S ribosomal protein L30 /


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SR32
#52: Protein 50S ribosomal protein L32 /


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A657HW13

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RNA chain , 6 types, 6 molecules BabXY8

#6: RNA chain 16S ribosomal RNA /


Mass: 497404.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)
#27: RNA chain 23S ribosomal RNA /


Mass: 941477.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)
#28: RNA chain 5S ribosomal RNA /


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)
#53: RNA chain mRNA / Messenger RNA


Mass: 3815.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)
#54: RNA chain Initiator tRNA


Mass: 24541.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)
#55: RNA chain Leucine tRNA


Mass: 27424.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)

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30S ribosomal protein ... , 20 types, 20 molecules CDEFGHIJKLMNOPQRSTUV

#7: Protein 30S ribosomal protein S2 / / Small ribosomal subunit protein uS2


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V0
#8: Protein 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A3S7D3V3
#9: Protein 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SR62
#10: Protein 30S ribosomal protein S5 /


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A5V7D7L3
#11: Protein 30S ribosomal protein S6, fully modified isoform / Ribosome


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02358
#12: Protein 30S ribosomal protein S7 / / Small ribosomal subunit protein uS7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02359
#13: Protein 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A829CDV3
#14: Protein 30S ribosomal protein S9 /


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A8E2LXD9
#15: Protein 30S ribosomal protein S10 /


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A836N8P1
#16: Protein 30S ribosomal protein S11 /


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A7U9G2M1
#17: Protein 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A0K0HEP7
#18: Protein 30S ribosomal protein S13 /


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SR52
#19: Protein 30S ribosomal protein S14 /


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A2S8DCV7
#20: Protein 30S ribosomal protein S15 /


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3SSQ7
#21: Protein 30S ribosomal protein S16 / / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7T3
#22: Protein 30S ribosomal protein S17 /


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: E3GBX2
#23: Protein 30S ribosomal protein S18 /


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A7L6DXG2
#24: Protein 30S ribosomal protein S19 /


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: A0A829ADD3
#25: Protein 30S ribosomal protein S20 / / Small ribosomal subunit protein bS20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7U7
#26: Protein 30S ribosomal protein S21 /


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: E9TH65

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Protein/peptide / Sugars , 2 types, 2 molecules A

#56: Protein/peptide Drosocin1


Type: Peptide-like / Class: Antimicrobial / Mass: 2204.579 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dwil\GK19342, Dwil_GK19342 / Production host: Escherichia coli BW25113 (bacteria) / References: UniProt: B4MNS1, BIRD: PRD_002425
#60: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 298 molecules

#57: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#58: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 293 / Source method: obtained synthetically / Formula: Mg
#59: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#61: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the elongating ribosome
Type: RIBOSOME / Entity ID: #1-#3, #7-#26, #31-#51, #53-#55 / Source: NATURAL
Molecular weightValue: 2.2 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
2100 mMPotassiumacetateC2H3KO21
325 mMMagnesiumacetateC4H6MgO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 8 OD260/mL
Specimen supportGrid material: COPPER / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 900 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
4CTFFIND4.1.14CTF correction
10RELION4initial Euler assignmentBeta
11RELION4final Euler assignmentbeta
12RELION4classificationbeta
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84697 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006154213
ELECTRON MICROSCOPYf_angle_d1.006230671
ELECTRON MICROSCOPYf_dihedral_angle_d15.01771885
ELECTRON MICROSCOPYf_chiral_restr0.04929413
ELECTRON MICROSCOPYf_plane_restr0.01812267

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