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- PDB-7nhn: VgaL, an antibiotic resistance ABCF, in complex with 70S ribosome... -

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Basic information

Entry
Database: PDB / ID: 7nhn
TitleVgaL, an antibiotic resistance ABCF, in complex with 70S ribosome from Listeria monocytogenes
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 27
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Lmo0919 protein
  • RNA (5'-R(P*GP*AP*GP*GP*UP*NP*NP*NP*NP*NP*NP*AP*UP*G)-3')
  • tRNA-fMet
KeywordsRIBOSOME / Antibiotic resistance element / ABCF / antibiotic resistance / ATPase / protein synthesis
Function / homology
Function and homology information


positive regulation of translational fidelity / ATPase-coupled transmembrane transporter activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit ...positive regulation of translational fidelity / ATPase-coupled transmembrane transporter activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / small 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 / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L31 type B / Ribosomal protein S14, type Z / 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 L31 type B / Ribosomal protein S14, type Z / 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 S14/S29 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / ABC transporter-like, conserved site / ABC transporters family signature. / 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 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 / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Ribosomal protein L14P, bacterial-type / Ribosomal protein S4, 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 / Ribosomal protein S15, bacterial-type / 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 S2 signature 2.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL31B ...ADENOSINE-5'-TRIPHOSPHATE / : / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32B / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL36 / 30S ribosomal protein S10 / 30S ribosomal protein S11 / 30S ribosomal protein S12 / 30S ribosomal protein S13 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S18 / 30S ribosomal protein S19 / 30S ribosomal protein S20 / 30S ribosomal protein S3 / 30S ribosomal protein S7 / 30S ribosomal protein S8 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL23 / 50S ribosomal protein L24 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / 30S ribosomal protein S5 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / 30S ribosomal protein S9 / 30S ribosomal protein S16 / 30S ribosomal protein S2 / 30S ribosomal protein S4 / Large ribosomal subunit protein bL21 / Lmo0919 protein / 30S ribosomal protein S6 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL30 / 30S ribosomal protein S15
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
Listeria monocytogenes EGD-E (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsCrowe-McAuliffe, C. / Turnbull, K.J. / Hauryliuk, V. / Wilson, D.N.
Funding support Germany, Sweden, Estonia, 6items
OrganizationGrant numberCountry
German Research Foundation (DFG)WI3285/8-1 Germany
Swedish Research Council2017-03783 Sweden
Swedish Research Council2019-01085 Sweden
European Regional Development Fund2014-2020.4.01.15-0013 Sweden
Estonian Research CouncilPRG335 Estonia
Swedish Research Council2018-00956 Sweden
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens.
Authors: Caillan Crowe-McAuliffe / Victoriia Murina / Kathryn Jane Turnbull / Marje Kasari / Merianne Mohamad / Christine Polte / Hiraku Takada / Karolis Vaitkevicius / Jörgen Johansson / Zoya ...Authors: Caillan Crowe-McAuliffe / Victoriia Murina / Kathryn Jane Turnbull / Marje Kasari / Merianne Mohamad / Christine Polte / Hiraku Takada / Karolis Vaitkevicius / Jörgen Johansson / Zoya Ignatova / Gemma C Atkinson / Alex J O'Neill / Vasili Hauryliuk / Daniel N Wilson /
Abstract: Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette ...Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F-subtype (ARE-ABCFs), which are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition from antibiotics that target the large ribosomal subunit. Here, we present single-particle cryo-EM structures of ARE-ABCF-ribosome complexes from three Gram-positive pathogens: Enterococcus faecalis LsaA, Staphylococcus haemolyticus VgaA and Listeria monocytogenes VgaL. Supported by extensive mutagenesis analysis, these structures enable a general model for antibiotic resistance mediated by these ARE-ABCFs to be proposed. In this model, ABCF binding to the antibiotic-stalled ribosome mediates antibiotic release via mechanistically diverse long-range conformational relays that converge on a few conserved ribosomal RNA nucleotides located at the peptidyltransferase center. These insights are important for the future development of antibiotics that overcome such target protection resistance mechanisms.
History
DepositionFeb 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 1, 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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Assembly

Deposited unit
0: Lmo0919 protein
D: tRNA-fMet
b: RNA (5'-R(P*GP*AP*GP*GP*UP*NP*NP*NP*NP*NP*NP*AP*UP*G)-3')
A: 23S rRNA
a: 16S rRNA
G: 50S ribosomal protein L2
H: 50S ribosomal protein L3
I: 50S ribosomal protein L4
J: 50S ribosomal protein L5
K: 50S ribosomal protein L6
M: 50S ribosomal protein L13
N: 50S ribosomal protein L14
O: 50S ribosomal protein L15
P: 50S ribosomal protein L16
Q: 50S ribosomal protein L17
R: 50S ribosomal protein L18
S: 50S ribosomal protein L19
T: 50S ribosomal protein L20
U: 50S ribosomal protein L21
V: 50S ribosomal protein L22
W: 50S ribosomal protein L23
X: 50S ribosomal protein L24
Z: 50S ribosomal protein L27
1: 50S ribosomal protein L28
2: 50S ribosomal protein L29
3: 50S ribosomal protein L30
5: 50S ribosomal protein L32-2
6: 50S ribosomal protein L33 1
7: 50S ribosomal protein L34
8: 50S ribosomal protein L35
9: 50S ribosomal protein L36
B: 5S rRNA
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
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 type Z
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
4: 50S ribosomal protein L31 type B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,206,885223
Polymers2,201,08752
Non-polymers5,798171
Water0
1


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

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Components

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Protein , 1 types, 1 molecules 0

#1: Protein Lmo0919 protein


Mass: 64280.094 Da / Num. of mol.: 1 / Mutation: E104Q, E408Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: lmo0919 / Production host: Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y8I3

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RNA chain , 5 types, 5 molecules DbAaB

#2: RNA chain tRNA-fMet


Mass: 24788.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria)
#3: RNA chain RNA (5'-R(P*GP*AP*GP*GP*UP*NP*NP*NP*NP*NP*NP*AP*UP*G)-3')


Mass: 3783.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria)
#4: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 949689.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria)
#5: RNA chain 16S rRNA /


Mass: 499378.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: GenBank: CP023861.1
#32: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 36692.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-E (bacteria)

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50S ribosomal protein ... , 27 types, 27 molecules GHIJKMNOPQRSTUVWXZ123567894

#6: Protein 50S ribosomal protein L2 /


Mass: 30568.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P60426
#7: Protein 50S ribosomal protein L3 /


Mass: 22863.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y440
#8: Protein 50S ribosomal protein L4 /


Mass: 22640.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P61055
#9: Protein 50S ribosomal protein L5 /


Mass: 20023.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q927L9
#10: Protein 50S ribosomal protein L6 /


Mass: 19434.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y444
#11: Protein 50S ribosomal protein L13 /


Mass: 16227.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y458
#12: Protein 50S ribosomal protein L14 /


Mass: 13248.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q927L7
#13: Protein 50S ribosomal protein L15 /


Mass: 15812.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y447
#14: Protein 50S ribosomal protein L16 /


Mass: 16171.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q927L4
#15: Protein 50S ribosomal protein L17 /


Mass: 15246.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y450
#16: Protein 50S ribosomal protein L18 /


Mass: 13121.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y445
#17: Protein 50S ribosomal protein L19 /


Mass: 13146.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: O53083
#18: Protein 50S ribosomal protein L20 /


Mass: 13719.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66103
#19: Protein 50S ribosomal protein L21 /


Mass: 11234.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y6Y9
#20: Protein 50S ribosomal protein L22 /


Mass: 12895.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q927L2
#21: Protein 50S ribosomal protein L23 /


Mass: 10935.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y441
#22: Protein 50S ribosomal protein L24 /


Mass: 11205.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y443
#23: Protein 50S ribosomal protein L27 /


Mass: 10571.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66125
#24: Protein 50S ribosomal protein L28 /


Mass: 7010.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66144
#25: Protein 50S ribosomal protein L29 /


Mass: 7414.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66166
#26: Protein 50S ribosomal protein L30 /


Mass: 6504.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q927M5
#27: Protein 50S ribosomal protein L32-2 / Ribosome


Mass: 6534.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66207
#28: Protein/peptide 50S ribosomal protein L33 1 / Ribosome


Mass: 6021.034 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66219
#29: Protein/peptide 50S ribosomal protein L34 /


Mass: 5319.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66248
#30: Protein 50S ribosomal protein L35 /


Mass: 7746.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P0A491
#31: Protein/peptide 50S ribosomal protein L36 /


Mass: 4336.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66290
#52: Protein 50S ribosomal protein L31 type B / Ribosome


Mass: 9274.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P0A485

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30S ribosomal protein ... , 19 types, 19 molecules cdefghijklmnopqrstu

#33: Protein 30S ribosomal protein S2 /


Mass: 28417.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y6M6
#34: Protein 30S ribosomal protein S3 /


Mass: 24587.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66548
#35: Protein 30S ribosomal protein S4 /


Mass: 22773.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y6T6
#36: Protein 30S ribosomal protein S5 /


Mass: 17482.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y446
#37: Protein 30S ribosomal protein S6 /


Mass: 11526.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8YAR9
#38: Protein 30S ribosomal protein S7 /


Mass: 17848.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66611
#39: Protein 30S ribosomal protein S8 /


Mass: 14667.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66623
#40: Protein 30S ribosomal protein S9 /


Mass: 14397.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y459
#41: Protein 30S ribosomal protein S10 /


Mass: 11703.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66330
#42: Protein 30S ribosomal protein S11 /


Mass: 13812.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66352
#43: Protein 30S ribosomal protein S12 /


Mass: 15216.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66372
#44: Protein 30S ribosomal protein S13 /


Mass: 13738.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66383
#45: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7164.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66401
#46: Protein 30S ribosomal protein S15 /


Mass: 10656.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q92C24
#47: Protein 30S ribosomal protein S16 /


Mass: 10386.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q8Y699
#48: Protein 30S ribosomal protein S17 /


Mass: 10057.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: Q927L6
#49: Protein 30S ribosomal protein S18 /


Mass: 9119.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66461
#50: Protein 30S ribosomal protein S19 /


Mass: 10498.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66484
#51: Protein 30S ribosomal protein S20 /


Mass: 9189.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria monocytogenes EGD-e (bacteria) / References: UniProt: P66503

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Non-polymers , 5 types, 171 molecules

#53: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#54: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 143 / Source method: obtained synthetically / Formula: Mg
#55: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#56: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: K
#57: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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: VgaL in complex with 70S ribosome, mRNA, and distorted P-tRNA from Listeria monocytogenes
Type: RIBOSOME / Entity ID: #1-#52 / Source: RECOMBINANT
Molecular weightValue: 2.2 MDa / Experimental value: NO
Source (natural)Organism: Listeria monocytogenes EGD-e (bacteria)
Source (recombinant)Organism: Listeria monocytogenes EGD-e (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 magnification: 165000 X / Nominal defocus max: -1900 nm / Nominal defocus min: -700 nm / Cs: 2.7 mm
Image recordingElectron dose: 26.3 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1

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Processing

EM softwareName: Gctf / Category: CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 83340
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45548 / Symmetry type: POINT

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