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- PDB-7m4x: A. baumannii Ribosome-Eravacycline complex: P-site tRNA 70S -

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Basic information

Entry
Database: PDB / ID: 7m4x
TitleA. baumannii Ribosome-Eravacycline complex: P-site tRNA 70S
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 28
  • 16s Ribosomal RNA
  • 23s ribosomal RNA
  • 5s ribosomal RNA
  • mRNAMessenger RNA
  • tRNA-met
KeywordsRIBOSOME/ANTIBIOTIC / Acinetobacter baumannii / ribosome / eravacycline / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / 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 S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L21, conserved site ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / 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 S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-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 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19
Similarity search - Domain/homology
Eravacycline / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / 30S ribosomal protein S10 ...Eravacycline / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / 30S ribosomal protein S10 / 30S ribosomal protein S11 / 30S ribosomal protein S21 / 30S ribosomal protein S18 / 50S ribosomal protein L14 / 50S ribosomal protein L30 / 50S ribosomal protein L33 / 50S ribosomal protein L28 / Small ribosomal subunit protein bS16 / 50S ribosomal protein L36 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL9 / 50S ribosomal protein L34 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL20
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsMorgan, C.E. / Yu, E.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: mBio / Year: 2021
Title: Cryo-EM Determination of Eravacycline-Bound Structures of the Ribosome and the Multidrug Efflux Pump AdeJ of Acinetobacter baumannii.
Authors: Zhemin Zhang / Christopher E Morgan / Robert A Bonomo / Edward W Yu /
Abstract: Antibiotic-resistant strains of the Gram-negative pathogen Acinetobacter baumannii have emerged as a significant global health threat. One successful therapeutic option to treat bacterial infections ...Antibiotic-resistant strains of the Gram-negative pathogen Acinetobacter baumannii have emerged as a significant global health threat. One successful therapeutic option to treat bacterial infections has been to target the bacterial ribosome. However, in many cases, multidrug efflux pumps within the bacterium recognize and extrude these clinically important antibiotics designed to inhibit the protein synthesis function of the bacterial ribosome. Thus, multidrug efflux within A. baumannii and other highly drug-resistant strains is a major cause of failure of drug-based treatments of infectious diseases. We here report the first structures of the cinetobacter rug fflux (Ade)J pump in the presence of the antibiotic eravacycline, using single-particle cryo-electron microscopy (cryo-EM). We also describe cryo-EM structures of the eravacycline-bound forms of the A. baumannii ribosome, including the 70S, 50S, and 30S forms. Our data indicate that the AdeJ pump primarily uses hydrophobic interactions to bind eravacycline, while the 70S ribosome utilizes electrostatic interactions to bind this drug. Our work here highlights how an antibiotic can bind multiple bacterial targets through different mechanisms and potentially enables drug optimization by taking advantage of these different modes of ligand binding. Acinetobacter baumannii has developed into a highly antibiotic-resistant Gram-negative pathogen. The prevalent AdeJ multidrug efflux pump mediates resistance to different classes of antibiotics known to inhibit the function of the 70S ribosome. Here, we report the first structures of the A. baumannii AdeJ pump, both in the absence and presence of eravacycline. We also describe structures of the A. baumannii ribosome bound by this antibiotic. Our results indicate that AdeJ and the ribosome use very distinct binding modes for drug recognition. Our work will ultimately enable structure-based drug discovery to combat antibiotic-resistant A. baumannii infection.
History
DepositionMar 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jun 9, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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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
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
a: 16s Ribosomal RNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
u: 30S ribosomal protein S21
v: tRNA-met
w: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,167,152247
Polymers2,160,79353
Non-polymers6,359194
Water9,944552
1


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

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Components

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50S ribosomal protein ... , 28 types, 28 molecules 0123CDEFGHIJKLMNOPQRSTUVWXYZ

#1: Protein 50S ribosomal protein L33 /


Mass: 6105.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: A0A062FI44
#2: Protein/peptide 50S ribosomal protein L34 /


Mass: 5192.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: N9JUR3
#3: Protein 50S ribosomal protein L35 /


Mass: 7424.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I693
#4: Protein/peptide 50S ribosomal protein L36 /


Mass: 4276.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: A0A372FJT1
#7: Protein 50S ribosomal protein L2 /


Mass: 30346.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA36
#8: Protein 50S ribosomal protein L3 /


Mass: 22512.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA39
#9: Protein 50S ribosomal protein L4 /


Mass: 21583.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA38
#10: Protein 50S ribosomal protein L5 /


Mass: 20051.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA27
#11: Protein 50S ribosomal protein L6 /


Mass: 19126.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA24
#12: Protein 50S ribosomal protein L9 /


Mass: 15800.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IBC3
#13: Protein 50S ribosomal protein L13 /


Mass: 15981.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I9B0
#14: Protein 50S ribosomal protein L14 /


Mass: 13523.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: A0A062FDM9
#15: Protein 50S ribosomal protein L15 /


Mass: 15509.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA20
#16: Protein 50S ribosomal protein L16 /


Mass: 15498.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA32
#17: Protein 50S ribosomal protein L17 /


Mass: 14022.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA13
#18: Protein 50S ribosomal protein L18 /


Mass: 12443.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA23
#19: Protein 50S ribosomal protein L19 /


Mass: 13619.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IAS9
#20: Protein 50S ribosomal protein L20 /


Mass: 13468.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: V5VGC9
#21: Protein 50S ribosomal protein L21 /


Mass: 11496.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I6V9
#22: Protein 50S ribosomal protein L22 /


Mass: 11828.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: A0A009I821
#23: Protein 50S ribosomal protein L23 /


Mass: 11607.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA37
#24: Protein 50S ribosomal protein L24 /


Mass: 11187.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA28
#25: Protein 50S ribosomal protein L25 /


Mass: 10942.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I7B6
#26: Protein 50S ribosomal protein L27 /


Mass: 9072.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I6V8
#27: Protein 50S ribosomal protein L28 /


Mass: 9125.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: A0A062FRJ6
#28: Protein 50S ribosomal protein L29 /


Mass: 7449.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA31
#29: Protein 50S ribosomal protein L30 /


Mass: 6654.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: A0A062FG91
#30: Protein 50S ribosomal protein L32 /


Mass: 7096.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I7A4

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RNA chain , 5 types, 5 molecules ABavw

#5: RNA chain 23s ribosomal RNA /


Mass: 945314.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057
#6: RNA chain 5s ribosomal RNA /


Mass: 36996.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: GenBank: 1577037162
#31: RNA chain 16s Ribosomal RNA /


Mass: 500296.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: GenBank: 1211343212
#52: RNA chain tRNA-met


Mass: 24760.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: GenBank: 1723902888
#53: RNA chain mRNA / Messenger RNA


Mass: 935.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057

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

#32: Protein 30S ribosomal protein S2 /


Mass: 27680.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: V5VBC2
#33: Protein 30S ribosomal protein S3 /


Mass: 27972.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: V5V9N0
#34: Protein 30S ribosomal protein S4 /


Mass: 23311.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA15
#35: Protein 30S ribosomal protein S5 /


Mass: 17181.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA22
#36: Protein 30S ribosomal protein S6 /


Mass: 14986.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IBC1
#37: Protein 30S ribosomal protein S7 /


Mass: 17733.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I7S0
#38: Protein 30S ribosomal protein S8 /


Mass: 14250.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA25
#39: Protein 30S ribosomal protein S9 /


Mass: 14287.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: V5VBA5
#40: Protein 30S ribosomal protein S10 /


Mass: 11718.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: A0A009L7S8
#41: Protein 30S ribosomal protein S11 /


Mass: 13558.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: A0A062DJ58
#42: Protein 30S ribosomal protein S12 /


Mass: 13797.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I7R9
#43: Protein 30S ribosomal protein S13 /


Mass: 13295.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA17
#44: Protein 30S ribosomal protein S14 /


Mass: 11438.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA26
#45: Protein 30S ribosomal protein S15 /


Mass: 10145.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I3U0
#46: Protein 30S ribosomal protein S16 /


Mass: 11223.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: A0A1V3DIZ9
#47: Protein 30S ribosomal protein S17 /


Mass: 9543.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA30
#48: Protein 30S ribosomal protein S18 /


Mass: 9009.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: A0A062FAE9
#49: Protein 30S ribosomal protein S19 /


Mass: 10206.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA35
#50: Protein 30S ribosomal protein S20 /


Mass: 9723.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I5N9
#51: Protein 30S ribosomal protein S21 /


Mass: 8474.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: A0A062DNQ5

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Non-polymers , 4 types, 746 molecules

#54: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#55: Chemical ChemComp-YQM / Eravacycline / Eravacycline


Mass: 558.555 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H31FN4O8 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 190 / Source method: obtained synthetically / Formula: Mg
#57: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 552 / 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: A baumannii 70S ribosome with P-site tRNA in complex with Eravacycline
Type: RIBOSOME / Entity ID: #1-#53 / Source: NATURAL
Source (natural)Organism: Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 46 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: cryoSPARC / Category: final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40679
Details: 50S resolution = 2.66. 30S core resolution = 2.78. 30S head resolution = 2.75.
Symmetry type: POINT

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