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- PDB-9ti6: Staphylococcus aureus 70S ribosome with p/E tRNA and RRF oriented... -

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Basic information

Entry
Database: PDB / ID: 9ti6
TitleStaphylococcus aureus 70S ribosome with p/E tRNA and RRF oriented towards the LSU (postTC-RRF-LSU)
Components
  • (30S ribosomal protein ...) x 18
  • (50S ribosomal protein ...) x 25
  • (Large ribosomal subunit protein ...) x 4
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • Ribosome-recycling factor
  • Small ribosomal subunit protein uS10
  • mRNA
  • tRNA(Ser3)
KeywordsRIBOSOME / RRF / EF-G / Recycling
Function / homology
Function and homology information


ribosomal large subunit binding / translational termination / large ribosomal subunit / transferase activity / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding ...ribosomal large subunit binding / translational termination / large ribosomal subunit / transferase activity / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / 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 / : ...Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / 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 L11, bacterial-type / Ribosomal protein L31 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 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 L11, N-terminal / Ribosomal protein L11, N-terminal domain / : / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / 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 L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S19, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L19, conserved site / 30S ribosomal protein S17 / Ribosomal protein L19 signature. / : / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S14/S29 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein S18, conserved site / Ribosomal L28 family / Ribosomal protein S18 signature. / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / Ribosomal protein L16
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL11 / 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 / Ribosome-recycling factor / 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 / 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 str. K-12 substr. MG1655 (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsGonzalez-Lopez, A. / Selmer, M.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Sven och Lilly Lawskis fond for naturvetenskaplig forskning Sweden
Uppsala Antibiotic Center Sweden
Swedish Research Council2022-04511 Sweden
CitationJournal: To Be Published
Title: Structural mechanism of ribosome recycling inhibited by fusidic acid
Authors: Gonzalez-Lopez, A. / Larsson, D.S.D. / Selmer, M.
History
DepositionDec 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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: 23S rRNA
B: 5S rRNA
C: Ribosome-recycling factor
D: tRNA(Ser3)
G: 50S ribosomal protein L2
H: 50S ribosomal protein L3
I: 50S ribosomal protein L4
J: 50S ribosomal protein L5
K: Large ribosomal subunit protein uL6
L: Large ribosomal subunit protein uL11
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
a: 16S rRNA
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)2,212,831179
Polymers2,209,67054
Non-polymers3,161125
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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50S ribosomal protein ... , 25 types, 25 molecules 1234789GHIJMNOPQRSTUVWXYZ

#1: 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
#2: 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
#3: 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
#4: Protein 50S ribosomal protein L31 type B


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
#7: 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
#8: 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
#9: 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
#14: 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
#15: 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
#16: 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
#17: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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

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Large ribosomal subunit protein ... , 4 types, 4 molecules 56KL

#5: 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)
References: UniProt: Q2FZF1
#6: 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)
References: UniProt: Q2FYU6
#18: Protein Large ribosomal subunit protein uL6 / 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
#19: Protein Large ribosomal subunit protein uL11 / 50S ribosomal protein L11


Mass: 14893.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: P0A0F4

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RNA chain , 5 types, 5 molecules ABDab

#10: RNA chain 23S rRNA


Mass: 946811.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
#11: RNA chain 5S rRNA


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
#13: RNA chain tRNA(Ser3)


Mass: 30258.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Production host: Escherichia coli (E. coli) / References: GenBank: 1845258627
#34: RNA chain 16S rRNA


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


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 Ck

#12: Protein Ribosome-recycling factor / RRF / Ribosome-releasing factor


Mass: 20576.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: frr, SAOUHSC_01236 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FZ21
#44: 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)
References: UniProt: A5IV35

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

#36: 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
#37: 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
#38: 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
#39: 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
#40: 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
#41: 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
#42: 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
#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
#45: 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
#46: 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
#47: 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
#48: Protein 30S ribosomal protein S14 type Z


Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW19
#49: 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
#50: 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
#51: 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
#52: 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
#53: 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
#54: 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

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Non-polymers , 2 types, 125 molecules

#55: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 122 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationN

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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: S. aureus 70S ribosome in complex with a tRNA and ribosome recycling factor (RRF)
Type: RIBOSOME / Entity ID: #1-#54 / Source: NATURAL
Molecular weightValue: 2.3 MDa / Experimental value: NO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES-KOHC8H18N2O4S-KOH1
295 mMPotassium chlorideKCl1
35 mMAmmonium chlorideNH4Cl1
45 mMMagnesium acetateMg(OAc)21
50.5 mMCalcium chlorideCaCl21
68 mMPutrescine(CH2)4(NH2)21
71 mMSpermidineC7H19N31
85 mMBeta-mercaptoethanolC2H6OS1
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 R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / 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 FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.45 sec. / Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 56478
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1-cuda12+250814particle selection
2EPUimage acquisition
4cryoSPARC4.7.1-cuda12+250814CTF correction
7Coot0.9.8.96model fitting
9cryoSPARC4.7.1-cuda12+250814initial Euler assignment
10cryoSPARC4.7.1-cuda12+250814final Euler assignment
11cryoSPARC4.7.1-cuda12+250814classification
12cryoSPARC4.7.1-cuda12+2508143D reconstruction
13Coot0.9.8.96model refinement
14Servalcat0.4.105model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2556350
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25462 / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeInitial refinement model-IDSource nameTypeDetails (eV)
19GHG

9ghg

9GHG1PDBexperimental model
2AlphaFoldin silico modelchain C and L
3AlphaFoldin silico modelchain L
RefinementResolution: 2.62→403.2 Å / Num. reflection obs: 7633303 / Average fsc work: 0.8295
Displacement parametersBiso mean: 55.88 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.00241544960.011
ELECTRON MICROSCOPYs_angle_nonh_deg0.78942306881.8461
ELECTRON MICROSCOPYs_dihedral_angle_1_deg4.556156875
ELECTRON MICROSCOPYs_dihedral_angle_2_deg1.825354655
ELECTRON MICROSCOPYs_dihedral_angle_3_deg8.66421307110
ELECTRON MICROSCOPYs_dihedral_angle_6_deg9.1106246310
ELECTRON MICROSCOPYs_chiral_restr0.0252294830.1174
ELECTRON MICROSCOPYs_planes0.00231358610.02
ELECTRON MICROSCOPYs_nbd0.18141690150.2
ELECTRON MICROSCOPYs_nbtor0.18371750380.2
ELECTRON MICROSCOPYs_hbond_nbd0.131653080.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.62-2.644ELECTRON MICROSCOPY2049810.6719
2.644-2.661ELECTRON MICROSCOPY1449430.6885
2.661-2.679ELECTRON MICROSCOPY1425850.6985
2.679-2.697ELECTRON MICROSCOPY1414170.7089
2.697-2.715ELECTRON MICROSCOPY1400950.7141
2.715-2.734ELECTRON MICROSCOPY1377930.7136
2.734-2.752ELECTRON MICROSCOPY1357810.7166
2.752-2.771ELECTRON MICROSCOPY1343610.7225
2.771-2.79ELECTRON MICROSCOPY1324870.7333
2.79-2.81ELECTRON MICROSCOPY1301770.7422
2.81-2.829ELECTRON MICROSCOPY1272090.7469
2.829-2.849ELECTRON MICROSCOPY1273510.7511
2.849-2.87ELECTRON MICROSCOPY1249530.7612
2.87-2.89ELECTRON MICROSCOPY1234090.7719
2.89-2.911ELECTRON MICROSCOPY1207090.782
2.911-2.932ELECTRON MICROSCOPY1191990.789
2.932-2.954ELECTRON MICROSCOPY1189090.7953
2.954-2.976ELECTRON MICROSCOPY1164810.8023
2.976-2.998ELECTRON MICROSCOPY1136470.8108
2.998-3.02ELECTRON MICROSCOPY1131570.8215
3.02-3.043ELECTRON MICROSCOPY1107610.8311
3.043-3.066ELECTRON MICROSCOPY1104970.84
3.066-3.089ELECTRON MICROSCOPY1069590.8477
3.09-3.113ELECTRON MICROSCOPY1062130.852
3.114-3.138ELECTRON MICROSCOPY1053330.8594
3.138-3.162ELECTRON MICROSCOPY1027510.8646
3.162-3.187ELECTRON MICROSCOPY1010250.8679
3.187-3.213ELECTRON MICROSCOPY990370.8709
3.213-3.238ELECTRON MICROSCOPY991270.8737
3.239-3.265ELECTRON MICROSCOPY962850.8753
3.265-3.291ELECTRON MICROSCOPY951250.8749
3.291-3.318ELECTRON MICROSCOPY936210.8746
3.319-3.346ELECTRON MICROSCOPY922150.874
3.346-3.374ELECTRON MICROSCOPY909010.8727
3.374-3.402ELECTRON MICROSCOPY883890.8735
3.403-3.431ELECTRON MICROSCOPY869470.874
3.432-3.461ELECTRON MICROSCOPY864930.8739
3.461-3.491ELECTRON MICROSCOPY849250.8711
3.491-3.521ELECTRON MICROSCOPY824970.8695
3.521-3.552ELECTRON MICROSCOPY820510.8713
3.552-3.584ELECTRON MICROSCOPY803290.8716
3.584-3.616ELECTRON MICROSCOPY789330.8715
3.616-3.649ELECTRON MICROSCOPY766990.8728
3.649-3.682ELECTRON MICROSCOPY759570.8757
3.682-3.716ELECTRON MICROSCOPY753250.8774
3.716-3.751ELECTRON MICROSCOPY731550.8775
3.751-3.786ELECTRON MICROSCOPY717970.8766
3.786-3.822ELECTRON MICROSCOPY702970.877
3.822-3.858ELECTRON MICROSCOPY702690.8771
3.858-3.896ELECTRON MICROSCOPY669430.8765
3.896-3.934ELECTRON MICROSCOPY668610.8798
3.934-3.972ELECTRON MICROSCOPY654970.8839
3.972-4.012ELECTRON MICROSCOPY640950.8819
4.012-4.052ELECTRON MICROSCOPY629050.8805
4.052-4.093ELECTRON MICROSCOPY610450.8792
4.093-4.135ELECTRON MICROSCOPY611490.879
4.135-4.178ELECTRON MICROSCOPY593830.8797
4.178-4.222ELECTRON MICROSCOPY579450.8803
4.222-4.266ELECTRON MICROSCOPY561610.8791
4.267-4.312ELECTRON MICROSCOPY553630.878
4.312-4.359ELECTRON MICROSCOPY542730.8765
4.359-4.406ELECTRON MICROSCOPY531730.8784
4.407-4.455ELECTRON MICROSCOPY518850.8787
4.455-4.505ELECTRON MICROSCOPY512950.8785
4.505-4.556ELECTRON MICROSCOPY498450.8801
4.556-4.608ELECTRON MICROSCOPY486370.8814
4.608-4.661ELECTRON MICROSCOPY472390.8796
4.661-4.715ELECTRON MICROSCOPY465690.8783
4.716-4.771ELECTRON MICROSCOPY457690.8796
4.772-4.828ELECTRON MICROSCOPY440670.8786
4.829-4.887ELECTRON MICROSCOPY432730.8796
4.887-4.947ELECTRON MICROSCOPY423330.879
4.947-5.008ELECTRON MICROSCOPY415930.8784
5.009-5.071ELECTRON MICROSCOPY400150.8776
5.072-5.136ELECTRON MICROSCOPY391890.881
5.136-5.202ELECTRON MICROSCOPY378610.8817
5.203-5.27ELECTRON MICROSCOPY374550.8824
5.271-5.34ELECTRON MICROSCOPY363730.882
5.341-5.411ELECTRON MICROSCOPY350130.8829
5.412-5.485ELECTRON MICROSCOPY348490.8825
5.486-5.561ELECTRON MICROSCOPY333430.8805
5.562-5.639ELECTRON MICROSCOPY328650.881
5.639-5.719ELECTRON MICROSCOPY312850.8812
5.719-5.8ELECTRON MICROSCOPY306030.8827
5.802-5.886ELECTRON MICROSCOPY303130.8824
5.886-5.973ELECTRON MICROSCOPY287410.8795
5.973-6.062ELECTRON MICROSCOPY284550.8783
6.063-6.155ELECTRON MICROSCOPY271570.88
6.156-6.251ELECTRON MICROSCOPY270450.8755
6.251-6.349ELECTRON MICROSCOPY257770.8723
6.351-6.451ELECTRON MICROSCOPY244350.8717
6.451-6.555ELECTRON MICROSCOPY242770.8718
6.556-6.664ELECTRON MICROSCOPY233170.8739
6.665-6.776ELECTRON MICROSCOPY228510.8788
6.777-6.891ELECTRON MICROSCOPY217450.8807
6.893-7.011ELECTRON MICROSCOPY210330.8834
7.012-7.135ELECTRON MICROSCOPY207130.8863
7.137-7.264ELECTRON MICROSCOPY196470.8889
7.265-7.397ELECTRON MICROSCOPY188410.8904
7.398-7.534ELECTRON MICROSCOPY182170.8915
7.537-7.679ELECTRON MICROSCOPY177270.8953
7.68-7.828ELECTRON MICROSCOPY171250.8976
7.831-7.981ELECTRON MICROSCOPY161250.8927
7.985-8.144ELECTRON MICROSCOPY158710.8902
8.146-8.312ELECTRON MICROSCOPY152250.8916
8.314-8.487ELECTRON MICROSCOPY145330.894
8.489-8.669ELECTRON MICROSCOPY137530.8958
8.671-8.858ELECTRON MICROSCOPY130590.8982
8.862-9.059ELECTRON MICROSCOPY129730.9008
9.064-9.267ELECTRON MICROSCOPY120210.9015
9.27-9.482ELECTRON MICROSCOPY117310.9083
9.488-9.714ELECTRON MICROSCOPY109810.9173
9.716-9.953ELECTRON MICROSCOPY107250.9234
9.956-10.205ELECTRON MICROSCOPY101170.926
10.208-10.47ELECTRON MICROSCOPY93750.9318
10.474-10.745ELECTRON MICROSCOPY91330.936
10.753-11.043ELECTRON MICROSCOPY85770.9383
11.048-11.354ELECTRON MICROSCOPY82270.9429
11.359-11.678ELECTRON MICROSCOPY75970.9482
11.688-12.032ELECTRON MICROSCOPY73770.9488
12.037-12.402ELECTRON MICROSCOPY69010.9505
12.408-12.795ELECTRON MICROSCOPY63030.9521
12.802-13.214ELECTRON MICROSCOPY60730.9528
13.221-13.654ELECTRON MICROSCOPY56130.9544
13.67-14.141ELECTRON MICROSCOPY52750.9538
14.15-14.655ELECTRON MICROSCOPY49810.9521
14.664-15.196ELECTRON MICROSCOPY45330.9535
15.218-15.803ELECTRON MICROSCOPY43030.9578
15.815-16.447ELECTRON MICROSCOPY40170.9605
16.461-17.146ELECTRON MICROSCOPY35650.9593
17.161-17.907ELECTRON MICROSCOPY33010.9626
17.924-18.718ELECTRON MICROSCOPY29910.9648
18.759-19.651ELECTRON MICROSCOPY28570.9633
19.674-20.657ELECTRON MICROSCOPY25170.9618
20.711-21.739ELECTRON MICROSCOPY21790.9671
21.803-23.012ELECTRON MICROSCOPY20850.9697
23.049-24.403ELECTRON MICROSCOPY18610.965
24.448-25.972ELECTRON MICROSCOPY16690.9599
26.136-27.757ELECTRON MICROSCOPY13110.963
27.823-29.724ELECTRON MICROSCOPY12490.9572
29.887-32.179ELECTRON MICROSCOPY10890.9441
32.386-34.962ELECTRON MICROSCOPY9070.9354
35.094-37.93ELECTRON MICROSCOPY7290.9405
38.444-42.267ELECTRON MICROSCOPY6250.9459
42.501-47.191ELECTRON MICROSCOPY5710.9505
47.518-53.405ELECTRON MICROSCOPY3810.9389
53.88-61.487ELECTRON MICROSCOPY3010.951
62.215-71.276ELECTRON MICROSCOPY2250.9657
73.614-87.985ELECTRON MICROSCOPY1750.9797
90.158-111.828ELECTRON MICROSCOPY1050.9892
116.394-142.553ELECTRON MICROSCOPY490.9873
164.606-403.2ELECTRON MICROSCOPY400.9173

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