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- PDB-6yss: Structure of the P+9 ArfB-ribosome complex in the post-hydrolysis... -

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Basic information

Entry
Database: PDB / ID: 6yss
TitleStructure of the P+9 ArfB-ribosome complex in the post-hydrolysis state
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 31
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Alternative stalled-ribosome rescue factor B
  • Api137
  • P-site tRNAPhe
  • mRNAMessenger RNA
KeywordsRIBOSOME / translation / rescue / release
Function / homology
Function and homology information


translation release factor activity / aminoacyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / stringent response / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / translational termination ...translation release factor activity / aminoacyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / stringent response / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / translation repressor activity / mature ribosome assembly / translational termination / translation repressor activity, mRNA regulatory element binding / polysomal ribosome / assembly of large subunit precursor of preribosome / ribosome assembly / DNA-templated transcription, termination / response to reactive oxygen species / regulation of cell growth / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / ribosome binding / ribosome biogenesis / large ribosomal subunit / ribosomal large subunit assembly / response to radiation / 5S rRNA binding / cytosolic small ribosomal subunit / small ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / hydrolase activity / translation / defense response to bacterium / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / RNA binding / zinc ion binding / extracellular region / metal ion binding / cytosol
Similarity search - Function
Apidaecin / Apidaecin / Prokaryotic-type class I peptide chain release factors signature. / RF-1 domain / Peptide chain release factor class I / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. ...Apidaecin / Apidaecin / Prokaryotic-type class I peptide chain release factors signature. / RF-1 domain / Peptide chain release factor class I / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L31 type A / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S16 signature. / Ribosomal protein S16, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L11, bacterial-type / Ribosomal protein L16 signature 1. / Ribosomal protein L6 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L17 signature. / Ribosomal protein L10 / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L10P / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11, C-terminal / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L5, bacterial-type / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L18, bacterial-type / Ribosomal protein L20 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L6, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S19, bacterial-type / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S20 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S13, bacterial-type / Ribosomal L28 family / Ribosomal protein S4, bacterial-type / Ribosomal protein L33 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L35
Similarity search - Domain/homology
50S ribosomal protein L23 / 50S ribosomal protein L28 / 50S ribosomal protein L29 / 50S ribosomal protein L32 / 50S ribosomal protein L33 / 50S ribosomal protein L34 / 50S ribosomal protein L35 / 50S ribosomal protein L36 / 50S ribosomal protein L9 / 50S ribosomal protein L13 ...50S ribosomal protein L23 / 50S ribosomal protein L28 / 50S ribosomal protein L29 / 50S ribosomal protein L32 / 50S ribosomal protein L33 / 50S ribosomal protein L34 / 50S ribosomal protein L35 / 50S ribosomal protein L36 / 50S ribosomal protein L9 / 50S ribosomal protein L13 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L17 / 50S ribosomal protein L22 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L24 / Apidaecin / 50S ribosomal protein L20 / 50S ribosomal protein L25 / 50S ribosomal protein L5 / 50S ribosomal protein L4 / 50S ribosomal protein L27 / 30S ribosomal protein S4 / 50S ribosomal protein L19 / 30S ribosomal protein S17 / RNA (> 1000) / RNA (> 100) / RNA (> 10) / RNA / : / Alternative stalled-ribosome rescue factor B / 50S ribosomal protein L10 / 30S ribosomal protein S7 / 30S ribosomal protein S18 / 30S ribosomal protein S10 / 30S ribosomal protein S19 / 30S ribosomal protein S3 / 30S ribosomal protein S8 / 50S ribosomal protein L11 / 30S ribosomal protein S5 / 30S ribosomal protein S13 / 30S ribosomal protein S11 / 30S ribosomal protein S9 / 30S ribosomal protein S15 / 30S ribosomal protein S21 / 30S ribosomal protein S16 / 30S ribosomal protein S2 / 30S ribosomal protein S20 / 30S ribosomal protein S12 / 30S ribosomal protein S14 / 50S ribosomal protein L15 / 50S ribosomal protein L31
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Apis mellifera (honey bee)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsChan, K.-H. / Petrychenko, V. / Mueller, C. / Maracci, C. / Holtkamp, W. / Wilson, D.N. / Fischer, N. / Rodnina, M.V.
CitationJournal: Nat Commun / Year: 2020
Title: Mechanism of ribosome rescue by alternative ribosome-rescue factor B.
Authors: Kai-Hsin Chan / Valentyn Petrychenko / Claudia Mueller / Cristina Maracci / Wolf Holtkamp / Daniel N Wilson / Niels Fischer / Marina V Rodnina /
Abstract: Alternative ribosome-rescue factor B (ArfB) rescues ribosomes stalled on non-stop mRNAs by releasing the nascent polypeptide from the peptidyl-tRNA. By rapid kinetics we show that ArfB selects ...Alternative ribosome-rescue factor B (ArfB) rescues ribosomes stalled on non-stop mRNAs by releasing the nascent polypeptide from the peptidyl-tRNA. By rapid kinetics we show that ArfB selects ribosomes stalled on short truncated mRNAs, rather than on longer mRNAs mimicking pausing on rare codon clusters. In combination with cryo-electron microscopy we dissect the multistep rescue pathway of ArfB, which first binds to ribosomes very rapidly regardless of the mRNA length. The selectivity for shorter mRNAs arises from the subsequent slow engagement step, as it requires longer mRNA to shift to enable ArfB binding. Engagement results in specific interactions of the ArfB C-terminal domain with the mRNA entry channel, which activates peptidyl-tRNA hydrolysis by the N-terminal domain. These data reveal how protein dynamics translate into specificity of substrate recognition and provide insights into the action of a putative rescue factor in mitochondria.
History
DepositionApr 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
5: 50S ribosomal protein L10
6: 50S ribosomal protein L31
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
I: 50S ribosomal protein L11
J: 50S ribosomal protein L13
K: 50S ribosomal protein L14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: 50S ribosomal protein L21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
U: 50S ribosomal protein L24
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
a: 16S ribosomal RNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
u: 30S ribosomal protein S21
v: Api137
w: P-site tRNAPhe
x: mRNA
y: Alternative stalled-ribosome rescue factor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,229,019449
Polymers2,219,43658
Non-polymers9,583391
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 31 types, 31 molecules 0123456CDEFGHIJKLMNOPQRSTUVWXYZ

#1: Protein 50S ribosomal protein L32 / / ribosomal protein bL32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N4
#2: Protein 50S ribosomal protein L33 / / ribosomal protein bL33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N9
#3: Protein/peptide 50S ribosomal protein L34 / / ribosomal protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7P5
#4: Protein 50S ribosomal protein L35 / / Ribosomal protein A / ribosomal protein bL35


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#5: Protein/peptide 50S ribosomal protein L36 / / Ribosomal protein B / ribosomal protein bL36


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q6
#6: Protein 50S ribosomal protein L10 /


Mass: 17736.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A073UC57
#7: Protein 50S ribosomal protein L31 /


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: U9XX47
#10: Protein 50S ribosomal protein L2 / / ribosomal protein uL2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60422
#11: Protein 50S ribosomal protein L3 / / ribosomal protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#12: Protein 50S ribosomal protein L4 / / ribosomal protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60723
#13: Protein 50S ribosomal protein L5 / / ribosomal protein uL5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P62399
#14: Protein 50S ribosomal protein L6 / / ribosomal protein uL6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#15: Protein 50S ribosomal protein L9 / / ribosomal protein bL9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R1
#16: Protein 50S ribosomal protein L11 / / ribosomal protein uL11


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J7
#17: Protein 50S ribosomal protein L13 / / ribosomal protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA10
#18: Protein 50S ribosomal protein L14 / / ribosomal protein uL14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3
#19: Protein 50S ribosomal protein L15 / / ribosomal protein uL15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02413
#20: Protein 50S ribosomal protein L16 / / ribosomal protein uL16


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7
#21: Protein 50S ribosomal protein L17 / / ribosomal protein uL17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#22: Protein 50S ribosomal protein L18 / / ribosomal protein uL18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#23: Protein 50S ribosomal protein L19 / / ribosomal protein bL19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K6
#24: Protein 50S ribosomal protein L20 / / ribosomal protein bL20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L3
#25: Protein 50S ribosomal protein L21 / / ribosomal protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG48
#26: Protein 50S ribosomal protein L22 / / ribosomal protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P61175
#27: Protein 50S ribosomal protein L23 / / ribosomal protein uL23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#28: Protein 50S ribosomal protein L24 / / ribosomal protein uL24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#29: Protein 50S ribosomal protein L25 / / ribosomal protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919
#30: Protein 50S ribosomal protein L27 / / ribosomal protein bL27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#31: Protein 50S ribosomal protein L28 / / ribosomal protein bL28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M2
#32: Protein 50S ribosomal protein L29 / / ribosomal protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M6
#33: Protein 50S ribosomal protein L30 / / ribosomal protein uL30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG51

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RNA chain , 5 types, 5 molecules ABawx

#8: RNA chain 23S ribosomal RNA /


Mass: 941518.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#9: RNA chain 5S ribosomal RNA /


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1726050194
#34: RNA chain 16S ribosomal RNA /


Mass: 499873.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#56: RNA chain P-site tRNAPhe


Mass: 24643.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#57: RNA chain mRNA / Messenger RNA


Mass: 4716.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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

#35: Protein 30S ribosomal protein S2 /


Mass: 26652.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3TPN2
#36: Protein 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQX2
#37: Protein 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR62
#38: Protein 30S ribosomal protein S5 /


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR27
#39: Protein 30S ribosomal protein S6 /


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#40: Protein 30S ribosomal protein S7 /


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A5Q2GFB5
#41: Protein 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR12
#42: Protein 30S ribosomal protein S9 /


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SRY2
#43: Protein 30S ribosomal protein S10 /


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQT7
#44: Protein 30S ribosomal protein S11 /


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR57
#45: Protein 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: I2UHF1
#46: Protein 30S ribosomal protein S13 /


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR52
#47: Protein 30S ribosomal protein S14 /


Mass: 11677.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: I2X5X6
#48: Protein 30S ribosomal protein S15 /


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SSQ7
#49: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SYP2
#50: Protein 30S ribosomal protein S17 /


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQY7
#51: Protein 30S ribosomal protein S18 /


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SFP7
#52: Protein 30S ribosomal protein S19 /


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQW2
#53: Protein 30S ribosomal protein S20 /


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3TRH7
#54: Protein 30S ribosomal protein S21 /


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3STZ7

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Protein/peptide / Protein , 2 types, 2 molecules vy

#55: Protein/peptide Api137


Mass: 1699.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Apis mellifera (honey bee) / References: UniProt: Q8WSY8
#58: Protein Alternative stalled-ribosome rescue factor B / Aminoacyl-tRNA hydrolase / Class I peptide chain release factor / Peptidyl-tRNA hydrolase ArfB / ...Aminoacyl-tRNA hydrolase / Class I peptide chain release factor / Peptidyl-tRNA hydrolase ArfB / Peptidyl-tRNA hydrolase YaeJ / Protein YaeJ / Putative peptidyl-tRNA hydrolase


Mass: 15656.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A024L8R9, aminoacyl-tRNA hydrolase

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Non-polymers , 3 types, 391 molecules

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


Mass: 24.305 Da / Num. of mol.: 387 / Source method: obtained synthetically / Formula: Mg
#60: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#61: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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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

Component
IDNameTypeEntity IDParent-IDSource
1Post-hydrolysis state of E. coli ribosome P+9 70S-ArfB-Api137-tRNAPhe-mRNA complexRIBOSOME#1-#580MULTIPLE SOURCES
2Post-hydrolysis state of E. coli ribosome P+9 70S-ArfB-Api137-tRNAPhe-mRNA complexCOMPLEX#1-#54, #56, #581NATURAL
3Post-hydrolysis state of E. coli ribosome P+9 70S-ArfB-Api137-tRNAPhe-mRNA complexCOMPLEX#551RECOMBINANT
4Post-hydrolysis state of E. coli ribosome P+9 70S-ArfB-Api137-tRNAPhe-mRNA complexCOMPLEX#571RECOMBINANT
Molecular weightValue: 2.6 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Apis mellifera (honey bee)7460
44Escherichia coli (E. coli)562
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13synthetic construct (others)32630
24synthetic construct (others)32630
Buffer solutionpH: 7.4 / Details: 50 mM HEPES, 30 mM KCl, 7 mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Custom-made glow-discharge instrument / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K / Details: Manual blotting & plunge-freezing

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Aberration corrections performed using Cs image corrector (CEOS company)
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 2.5 nm / Nominal defocus min: 200 nm / Calibrated defocus min: 200 nm / Calibrated defocus max: 2.5 nm / Cs: 0.01 mm / C2 aperture diameter: 100 µm / Alignment procedure: OTHER
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1
Details: Images were collected in movie mode at 40 fractions per image per second
EM imaging opticsSpherical aberration corrector: Cs image corrector (CEOS company)
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: UCSF ChimeraX / Version: 0.93/v8 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4GctfCTF correction
7UCSF Chimera0.91model fittingChimeraX
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 968783
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 282252 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building
IDPDB-ID 3D fitting-ID
15AFI1
24RB7

4rb7
PDB Unreleased entry

1
35O2R1
44V951

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