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- PDB-7nhl: VgaA-LC, an antibiotic resistance ABCF, in complex with 70S ribos... -

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Basic information

Entry
Database: PDB / ID: 7nhl
TitleVgaA-LC, an antibiotic resistance ABCF, in complex with 70S ribosome from Staphylococcus aureus
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 28
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • Lincosamide-streptogramin A resistance protein
  • P-tRNA fMet
  • RNA (5'-R(P*GP*GP*AP*GP*GP*UP*AP*UP*G)-3')
KeywordsRIBOSOME / Antibiotic resistance element / ABCF / antibiotic resistance / ATPase / protein synthesis
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit ...ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / 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 / RNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
ABC-transporter extension domain / ABC transporter / Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein L31 signature. / Ribosomal protein L31 ...ABC-transporter extension domain / ABC transporter / Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / 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 L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / 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 / ABC transporter / ABC transporter-like, ATP-binding domain / Ribosomal protein S13, bacterial-type / ATP-binding cassette, ABC transporter-type domain profile. / 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 / Ribosomal protein S15, bacterial-type / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L32 / 30S ribosomal protein S10 ...ADENOSINE-5'-TRIPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L32 / 30S ribosomal protein S10 / Lincosamide-streptogramin A resistance protein / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL31B / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL33B / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesStaphylococcus haemolyticus (bacteria)
Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsCrowe-McAuliffe, C. / Murina, V. / 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

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-12332
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Structure viewerMolecule:
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Assembly

Deposited unit
0: Lincosamide-streptogramin A resistance protein
D: P-tRNA fMet
Z: 50S ribosomal protein L27
P: 50S ribosomal protein L16
A: 23S rRNA
a: 16S rRNA
B: 5S 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
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
Y: 50S ribosomal protein L25
1: 50S ribosomal protein L28
2: 50S ribosomal protein L29
3: 50S ribosomal protein L30
6: 50S ribosomal protein L33 2
8: 50S ribosomal protein L35
7: 50S ribosomal protein L34
d: 30S ribosomal protein S3
e: 30S ribosomal protein S4
h: 30S ribosomal protein S7
k: 30S ribosomal protein S10
l: 30S ribosomal protein S11
o: 30S ribosomal protein S14 type Z
p: 30S ribosomal protein S15
q: 30S ribosomal protein S16
u: 30S ribosomal protein S20
9: 50S ribosomal protein L36
t: 30S ribosomal protein S19
n: 30S ribosomal protein S13
j: 30S ribosomal protein S9
f: 30S ribosomal protein S5
i: 30S ribosomal protein S8
s: 30S ribosomal protein S18
g: 30S ribosomal protein S6
b: RNA (5'-R(P*GP*GP*AP*GP*GP*UP*AP*UP*G)-3')
m: 30S ribosomal protein S12
r: 30S ribosomal protein S17
c: 30S ribosomal protein S2
4: 50S ribosomal protein L31 type B
5: 50S ribosomal protein L32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,231,635215
Polymers2,226,30153
Non-polymers5,334162
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: tRNA microarray and elements of the map support an initiation complex.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area274060 Å2
ΔGint-3438 kcal/mol
Surface area784950 Å2
MethodPISA

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Components

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Protein , 1 types, 1 molecules 0

#1: Protein Lincosamide-streptogramin A resistance protein


Mass: 63265.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus haemolyticus (bacteria) / Gene: vga(A)LC
Production host: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain (production host): SH1000 / References: UniProt: A0SNL9

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RNA chain , 5 types, 5 molecules DAaBb

#2: RNA chain P-tRNA fMet


Mass: 24506.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
#5: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 946696.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: GenBank: 87201381
#6: RNA chain 16S rRNA /


Mass: 501711.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: GenBank: CP000253.1
#7: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 36974.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: GenBank: CP000253.1
#48: RNA chain RNA (5'-R(P*GP*GP*AP*GP*GP*UP*AP*UP*G)-3')


Mass: 4128.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)

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50S ribosomal protein ... , 28 types, 28 molecules ZPGHIJKMNOQRSTUVWXY123687945

#3: Protein 50S ribosomal protein L27 /


Mass: 10334.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXT0
#4: Protein 50S ribosomal protein L16 /


Mass: 16274.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW13
#8: Protein 50S ribosomal protein L2 /


Mass: 30217.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: P60430
#9: Protein 50S ribosomal protein L3 /


Mass: 23760.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW06
#10: Protein 50S ribosomal protein L4 /


Mass: 22495.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW07
#11: Protein 50S ribosomal protein L5 /


Mass: 20296.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW18
#12: Protein 50S ribosomal protein L6 /


Mass: 19818.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW21
#13: Protein 50S ribosomal protein L13 /


Mass: 16359.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW38
#14: Protein 50S ribosomal protein L14 /


Mass: 13157.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW16
#15: Protein 50S ribosomal protein L15 /


Mass: 15628.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: P0A0F8
#16: Protein 50S ribosomal protein L17 /


Mass: 13771.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW33
#17: Protein 50S ribosomal protein L18 /


Mass: 13124.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW22
#18: Protein 50S ribosomal protein L19 /


Mass: 13392.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FZ42
#19: Protein 50S ribosomal protein L20 /


Mass: 13720.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXQ1
#20: Protein 50S ribosomal protein L21 /


Mass: 11354.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXS8
#21: Protein 50S ribosomal protein L22 /


Mass: 12857.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW11
#22: Protein 50S ribosomal protein L23 /


Mass: 10625.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW08
#23: Protein 50S ribosomal protein L24 /


Mass: 11561.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW17
#24: Protein 50S ribosomal protein L25 / / General stress protein CTC


Mass: 23810.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2G0S0
#25: Protein 50S ribosomal protein L28 /


Mass: 6995.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FZ60
#26: Protein 50S ribosomal protein L29 /


Mass: 8105.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW14
#27: Protein 50S ribosomal protein L30 /


Mass: 6565.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: P0A0G2
#28: Protein/peptide 50S ribosomal protein L33 2 / Ribosome


Mass: 5885.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FY22
#29: Protein 50S ribosomal protein L35 /


Mass: 7722.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXQ0
#30: Protein/peptide 50S ribosomal protein L34 /


Mass: 5454.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FUQ0
#40: Protein/peptide 50S ribosomal protein L36 /


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW29
#52: Protein 50S ribosomal protein L31 type B / Ribosome


Mass: 9737.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FWD8
#53: Protein 50S ribosomal protein L32 /


Mass: 6500.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: A0A0D1H2J5

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

#31: Protein 30S ribosomal protein S3 /


Mass: 24143.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW12
#32: Protein 30S ribosomal protein S4 /


Mass: 23051.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXK6
#33: Protein 30S ribosomal protein S7 /


Mass: 17826.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: P48940
#34: Protein 30S ribosomal protein S10 /


Mass: 11598.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: A0A0D1JTN2
#35: Protein 30S ribosomal protein S11 /


Mass: 13907.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW31
#36: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7246.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW19
#37: Protein 30S ribosomal protein S15 /


Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2G2Q1
#38: Protein 30S ribosomal protein S16 /


Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FZ45
#39: Protein 30S ribosomal protein S20 /


Mass: 9039.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXY6
#41: Protein 30S ribosomal protein S19 /


Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW10
#42: Protein 30S ribosomal protein S13 /


Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW30
#43: Protein 30S ribosomal protein S9 /


Mass: 14856.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW39
#44: Protein 30S ribosomal protein S5 /


Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW23
#45: Protein 30S ribosomal protein S8 /


Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW20
#46: Protein 30S ribosomal protein S18 /


Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2G111
#47: Protein 30S ribosomal protein S6 /


Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2G113
#49: Protein 30S ribosomal protein S12 /


Mass: 15320.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: P0A0H0
#50: Protein 30S ribosomal protein S17 /


Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW15
#51: Protein 30S ribosomal protein S2 /


Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FZ25

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Non-polymers , 4 types, 162 molecules

#54: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 138 / Source method: obtained synthetically / Formula: Mg
#55: 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
#56: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: K
#57: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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

Component
IDNameTypeEntity IDParent-IDSource
1VgaA-LC in complex with 70S ribosome, mRNA, and distorted P-tRNA from Staphylococcus aureusCOMPLEX#1-#530MULTIPLE SOURCES
270S ribosomeRibosomeRIBOSOME#2-#531NATURAL
3VgaA-LCCOMPLEX#11RECOMBINANT
Molecular weightValue: 2.2 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)93061
33Staphylococcus haemolyticus (bacteria)1283
Source (recombinant)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: SH1000
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: 165872
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61910 / Num. of class averages: 1 / Symmetry type: POINT

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