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- PDB-8p2g: Staphylococcus aureus 70S ribosome with elongation factor G locke... -

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Basic information

Entry
Database: PDB / ID: 8p2g
TitleStaphylococcus aureus 70S ribosome with elongation factor G locked with fusidic acid cyclopentane with a tRNA in pe/E chimeric state
Components
  • (30S ribosomal protein ...) x 18
  • (50S ribosomal protein ...) x 26
  • (Large ribosomal subunit protein ...) x 2
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Elongation factor GEF-G
  • Small ribosomal subunit protein uS10
  • mRNAMessenger RNA
  • tRNATransfer RNA
KeywordsRIBOSOME / fusidic acid / EF-G / antibiotic
Function / homology
Function and homology information


ribosome disassembly / translation elongation factor activity / 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 / small ribosomal subunit / cytoplasmic translation ...ribosome disassembly / translation elongation factor activity / 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 / 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 / GTPase activity / GTP binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L31 type B / : / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV ...Ribosomal protein L31 type B / : / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Ribosomal protein L25, long-form / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S14, type Z / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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 L32p, bacterial type / 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 / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / 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
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / 1,4-DIAMINOBUTANE / SPERMIDINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...GUANOSINE-5'-DIPHOSPHATE / 1,4-DIAMINOBUTANE / SPERMIDINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS10 / 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 bL33A / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Elongation factor G / 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 aureus subsp. aureus NCTC 8325 (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.02 Å
AuthorsGonzalez-Lopez, A. / Selmer, M.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Other private Sweden
Other government Sweden
Swedish Research Council2016-06264 Sweden
Swedish Research Council2022-04511 Sweden
CitationJournal: To Be Published
Title: Cryo-EM structures of Staphylococcus aureus 70S ribosomes in complex with elongation factor G and fusidic acid
Authors: Gonzalez-Lopez, A. / Larsson, D. / Nelson, B. / Hergenrother, P.J. / Selmer, M.
History
DepositionMay 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 23S ribosomal RNA
B: 5S ribosomal RNA
D: tRNA
E: Elongation factor G
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
Y: 50S ribosomal protein L25
Z: 50S ribosomal protein L27
1: 50S ribosomal protein L28
2: 50S ribosomal protein L29
3: 50S ribosomal protein L30
4: 50S ribosomal protein L31 type B
5: Large ribosomal subunit protein bL32
6: Large ribosomal subunit protein bL33A
7: 50S ribosomal protein L34
8: 50S ribosomal protein L35
9: 50S ribosomal protein L36
a: 16S ribosomal RNA
b: mRNA
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: Small ribosomal subunit protein uS10
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,251,233231
Polymers2,245,41553
Non-polymers5,818178
Water57,0903169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area278460 Å2
ΔGint-3673 kcal/mol
Surface area774500 Å2

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Components

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RNA chain , 5 types, 5 molecules ABDab

#1: RNA chain 23S ribosomal RNA /


Mass: 946782.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: 8324-4 / References: GenBank: CP000253
#2: RNA chain 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)
Strain: 8324-4 / References: GenBank: CP000253.1
#3: RNA chain tRNA / Transfer RNA


Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1848851804
#33: RNA chain 16S ribosomal RNA /


Mass: 503117.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: 8325-4 / References: GenBank: CP000253
#34: RNA chain mRNA / Messenger RNA


Mass: 7889.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Protein , 2 types, 2 molecules Ek

#4: Protein Elongation factor G / EF-G / EF-G


Mass: 76699.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: fusA, SAOUHSC_00529 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G0N1
#43: Protein Small ribosomal subunit protein uS10 / 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)
Strain: 8325-4 / References: UniProt: A5IV35

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50S ribosomal protein ... , 26 types, 26 molecules GHIJKMNOPQRSTUVWXYZ1234789

#5: 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)
Strain: 8325-4 / References: UniProt: P60430
#6: 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)
Strain: 8325-4 / References: UniProt: Q2FW06
#7: 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)
Strain: 8325-4 / References: UniProt: Q2FW07
#8: 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)
Strain: 8325-4 / References: UniProt: Q2FW18
#9: 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)
Strain: 8325-4 / References: UniProt: Q2FW21
#10: 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)
Strain: 8325-4 / References: UniProt: Q2FW38
#11: 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)
Strain: 8325-4 / References: UniProt: Q2FW16
#12: 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)
Strain: 8325-4 / References: UniProt: P0A0F8
#13: 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)
Strain: 8325-4 / References: UniProt: Q2FW13
#14: 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)
Strain: 8325-4 / References: UniProt: Q2FW33
#15: 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)
Strain: 8325-4 / References: UniProt: Q2FW22
#16: 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)
Strain: 8325-4 / References: UniProt: Q2FZ42
#17: 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)
Strain: 8325-4 / References: UniProt: Q2FXQ1
#18: 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)
Strain: 8325-4 / References: UniProt: Q2FXS8
#19: 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)
Strain: 8325-4 / References: UniProt: Q2FW11
#20: 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)
Strain: 8325-4 / References: UniProt: Q2FW08
#21: 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)
Strain: 8325-4 / References: UniProt: Q2FW17
#22: 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)
Strain: 8325-4 / References: UniProt: Q2G0S0
#23: 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)
Strain: 8325-4 / References: UniProt: Q2FXT0
#24: 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)
Strain: 8325-4 / References: UniProt: Q2FZ60
#25: 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)
Strain: 8325-4 / References: UniProt: Q2FW14
#26: 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)
Strain: 8325-4 / References: UniProt: P0A0G2
#27: 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)
Strain: 8325-4 / References: UniProt: Q2FWD8
#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)
Strain: 8325-4 / References: UniProt: Q2FUQ0
#31: 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)
Strain: 8325-4 / References: UniProt: Q2FXQ0
#32: 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)
Strain: 8325-4 / References: UniProt: Q2FW29

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Large ribosomal subunit protein ... , 2 types, 2 molecules 56

#28: Protein Large ribosomal subunit protein bL32 / 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)
Strain: 8325-4 / References: UniProt: Q2FZF1
#29: Protein/peptide Large ribosomal subunit protein bL33A / 50S ribosomal protein L33 1


Mass: 5944.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: 8325-4 / References: UniProt: Q2FYU6

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30S ribosomal protein ... , 18 types, 18 molecules cdefghijlmnopqrstu

#35: 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)
Strain: 8325-4 / References: UniProt: Q2FZ25
#36: 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)
Strain: 8325-4 / References: UniProt: Q2FW12
#37: 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)
Strain: 8325-4 / References: UniProt: Q2FXK6
#38: 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)
Strain: 8325-4 / References: UniProt: Q2FW23
#39: 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)
Strain: 8325-4 / References: UniProt: Q2G113
#40: 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)
Strain: 8325-4 / References: UniProt: P48940
#41: 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)
Strain: 8325-4 / References: UniProt: Q2FW20
#42: 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)
Strain: 8325-4 / References: UniProt: Q2FW39
#44: 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)
Strain: 8325-4 / References: UniProt: Q2FW31
#45: 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)
Strain: 8325-4 / References: UniProt: P0A0H0
#46: 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)
Strain: 8325-4 / References: UniProt: Q2FW30
#47: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: 8325-4 / References: UniProt: Q2FW19
#48: 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)
Strain: 8325-4 / References: UniProt: Q2G2Q1
#49: 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)
Strain: 8325-4 / References: UniProt: Q2FZ45
#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)
Strain: 8325-4 / References: UniProt: Q2FW15
#51: 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)
Strain: 8325-4 / References: UniProt: Q2G111
#52: 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)
Strain: 8325-4 / References: UniProt: Q2FW10
#53: 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)
Strain: 8325-4 / References: UniProt: Q2FXY6

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Non-polymers , 7 types, 3347 molecules

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


Mass: 24.305 Da / Num. of mol.: 169 / 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.: 3 / Source method: obtained synthetically / Formula: C7H19N3
#56: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE / Putrescine


Mass: 88.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N2
#57: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#58: Chemical ChemComp-WUX / 2-[(3~{R},4~{S},5~{S},8~{S},9~{S},10~{S},11~{R},13~{S},14~{S},16~{S})-16-acetyloxy-4,8,10,14-tetramethyl-3,11-bis(oxidanyl)-1,2,3,4,5,6,7,9,11,12,13,15,16,17-tetradecahydrocyclopenta[a]phenanthren-17-yl]-5-cyclopentyl-pentanoic acid


Mass: 546.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H54O6 / Feature type: SUBJECT OF INVESTIGATION
#59: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#60: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3169 / 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: Staphylococcus aureus 70S ribosome with elongation factor G and fusidic acid cyclopentane
Type: RIBOSOME / Entity ID: #24-#32, #1-#23, #33-#53 / Source: MULTIPLE SOURCES
Molecular weightValue: 2.6 MDa / Experimental value: NO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: 8325-4
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES-KOHC8H18N2O4S1
295 mMPotassium chlorideKCl1
35 mMAmmonium chlorideNH4Cl1
45 mMMagnesium acetateMg(OAc)21
50.5 mMCalcium chlorideCaCl21
68 mMPutrescine(CH2)4(NH2)21
71 mMSpermidineC7H19N31
80.4 mMFusidic acid cyclopentaneC33H50O6Na1
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 R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS 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: 1300 nm / Nominal defocus min: 700 nm / Calibrated defocus min: 200 nm / Calibrated defocus max: 2400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.23 sec. / Electron dose: 27.77 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17252
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.0.2particle selection
2EPU3.2.0image acquisition
4cryoSPARC4.0.2CTF correction
7UCSF ChimeraX1.5model fitting
9cryoSPARC4.0.2initial Euler assignment
10cryoSPARC4.1.2final Euler assignment
11cryoSPARC4.1.2classification
12cryoSPARC4.1.23D reconstruction
19Coot0.9.8.5model refinement
20PHENIX1.20.1-4487-000model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 559995
3D reconstructionResolution: 2.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 303005 / Algorithm: FOURIER SPACE / Num. of class averages: 9 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDChain-ID
17NHM

7nhm

7NHM1
22XEX

2xex

E2XEX2E
37SSD

7ssd

D7SSD3D
RefinementCross valid method: NONE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046158729
ELECTRON MICROSCOPYf_angle_d0.7151236912
ELECTRON MICROSCOPYf_chiral_restr0.043230223
ELECTRON MICROSCOPYf_plane_restr0.010513154
ELECTRON MICROSCOPYf_dihedral_angle_d13.115674172

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