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- PDB-7qgr: Structure of the SmrB-bound E. coli disome - collided 70S ribosome -

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Basic information

Entry
Database: PDB / ID: 7qgr
TitleStructure of the SmrB-bound E. coli disome - collided 70S ribosome
Components
  • (30S ribosomal protein ...) x 21
  • (50S ribosomal protein ...) x 31
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • A-site tRNA
  • P-site tRNA
  • UPF0115 protein YfcN
  • mRNA
KeywordsRIBOSOME / Ribosome rescue / disome / ribosome collision / stalling / no-go complex / nuclease / SmrB
Function / homology
Function and homology information


stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translational termination / four-way junction DNA binding ...stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translational termination / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / transcription elongation factor complex / DNA endonuclease activity / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / transcription antitermination / response to reactive oxygen species / DNA-templated transcription termination / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / endonuclease activity / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Uncharacterised protein family UPF0115 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. / Ribosomal protein S1 / Ribosomal protein S1-like / RNA-binding domain, S1 / Ribosomal protein L1, bacterial-type ...Uncharacterised protein family UPF0115 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. / Ribosomal protein S1 / Ribosomal protein S1-like / RNA-binding domain, S1 / Ribosomal protein L1, bacterial-type / S1 domain profile. / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / S1 RNA binding domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / 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, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 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 L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein L27 signature. / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site
Similarity search - Domain/homology
: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 ...: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / 50S ribosomal protein L31 / 30S ribosomal protein S9 / 30S ribosomal protein S18 / 30S ribosomal protein S5 / 50S ribosomal protein L1 / Small ribosomal subunit protein uS13 / 30S ribosomal protein S17 / 30S ribosomal protein S11 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / 30S ribosomal protein S1 / 50S ribosomal protein L3 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25 / UPF0115 protein YfcN / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein bL27
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Vibrio alginolyticus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsKratzat, H. / Buschauer, R. / Berninghausen, O. / Beckmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nature / Year: 2022
Title: Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria.
Authors: Kazuki Saito / Hanna Kratzat / Annabelle Campbell / Robert Buschauer / A Maxwell Burroughs / Otto Berninghausen / L Aravind / Rachel Green / Roland Beckmann / Allen R Buskirk /
Abstract: Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled ...Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes. Here, using a genetic screen in Escherichia coli, we discovered a new rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNAs) to rescue upstream ribosomes. SmrB is recruited to ribosomes and is activated by collisions. Cryo-electron microscopy structures of collided disomes from E. coli and Bacillus subtilis show distinct and conserved arrangements of individual ribosomes and the composite SmrB-binding site. These findings reveal the underlying mechanisms by which ribosome collisions trigger ribosome rescue in bacteria.
History
DepositionDec 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: 5S rRNA
P: 50S ribosomal protein L2
Q: 50S ribosomal protein L3
R: 50S ribosomal protein L4
S: 50S ribosomal protein L5
T: 50S ribosomal protein L6
V: 50S ribosomal protein L11
W: 50S ribosomal protein L13
X: 50S ribosomal protein L14
Y: 50S ribosomal protein L15
Z: 50S ribosomal protein L16
a: 50S ribosomal protein L17
b: 50S ribosomal protein L18
c: 50S ribosomal protein L19
d: 50S ribosomal protein L20
e: 50S ribosomal protein L21
f: 50S ribosomal protein L22
g: 50S ribosomal protein L23
h: 50S ribosomal protein L24
i: 50S ribosomal protein L25
j: 50S ribosomal protein L27
k: 50S ribosomal protein L28
l: 50S ribosomal protein L29
m: 50S ribosomal protein L30
n: 50S ribosomal protein L32
o: 50S ribosomal protein L33
p: 50S ribosomal protein L34
q: 50S ribosomal protein L35
r: 50S ribosomal protein L36
N: 23S rRNA
L: 50S ribosomal protein L31
C: 50S ribosomal protein L1
U: 50S ribosomal protein L9
M: P-site tRNA
x: mRNA
0: 16S rRNA
1: 30S ribosomal protein S2
2: 30S ribosomal protein S3
3: 30S ribosomal protein S4
4: 30S ribosomal protein S5
5: 30S ribosomal protein S6, non-modified isoform
6: 30S ribosomal protein S7
7: 30S ribosomal protein S8
8: 30S ribosomal protein S9
9: 30S ribosomal protein S10
A: 30S ribosomal protein S11
B: 30S ribosomal protein S12
D: 30S ribosomal protein S13
E: 30S ribosomal protein S14
F: 30S ribosomal protein S15
G: 30S ribosomal protein S16
H: 30S ribosomal protein S17
I: 30S ribosomal protein S18
J: 30S ribosomal protein S19
K: 30S ribosomal protein S20
s: 30S ribosomal protein S21
t: 30S ribosomal protein S1
u: A-site tRNA
v: UPF0115 protein YfcN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,524,49262
Polymers2,524,40559
Non-polymers883
Water1629
1


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

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Components

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RNA chain , 6 types, 6 molecules ONMx0u

#1: RNA chain 5S rRNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: CP035706.1
#30: RNA chain 23S rRNA


Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 170787319
#34: RNA chain P-site tRNA


Mass: 24060.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1207385735
#35: RNA chain mRNA


Mass: 221443.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio alginolyticus (bacteria)
#36: RNA chain 16S rRNA


Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1359176725
#58: RNA chain A-site tRNA


Mass: 23545.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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50S ribosomal protein ... , 31 types, 31 molecules PQRSTVWXYZabcdefghijklmnopqrLCU

#2: 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
#3: Protein 50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A829E125
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: Protein 50S ribosomal protein L17


Mass: 14335.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A829CNM8
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: Protein 50S ribosomal protein L23


Mass: 11252.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A829CFV1
#19: 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
#20: 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
#21: Protein 50S ribosomal protein L27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: V0A6S2
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: Protein 50S ribosomal protein L36


Mass: 6315.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#31: Protein 50S ribosomal protein L31


Mass: 7917.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A1X3HZV8
#32: Protein 50S ribosomal protein L1


Mass: 23735.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A4Y8DMK0
#33: 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

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30S ribosomal protein ... , 21 types, 21 molecules 123456789ABDEFGHIJKst

#37: Protein 30S ribosomal protein S2 / Small ribosomal subunit protein uS2


Mass: 26581.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0
#38: Protein 30S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 24293.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3
#39: 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
#40: Protein 30S ribosomal protein S5


Mass: 17120.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A377C6M5
#41: Protein 30S ribosomal protein S6, non-modified isoform


Mass: 15201.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#42: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 16992.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#43: 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
#44: Protein 30S ribosomal protein S9


Mass: 14872.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A1Z3UZ18
#45: Protein 30S ribosomal protein S10 / Small ribosomal subunit protein uS10 / Transcription termination/antitermination protein NusE


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R5
#46: Protein 30S ribosomal protein S11


Mass: 13844.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A829AF87
#47: 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: C3SQR7
#48: Protein 30S ribosomal protein S13


Mass: 13096.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: 4-5675286 / References: UniProt: A0A7U9IV78
#49: Protein 30S ribosomal protein S14


Mass: 11562.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A090BZT4
#50: Protein 30S ribosomal protein S15 / Small ribosomal subunit protein uS15


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#51: Protein 30S ribosomal protein S16 / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T3
#52: Protein 30S ribosomal protein S17


Mass: 9694.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A829A8C6
#53: Protein 30S ribosomal protein S18


Mass: 9006.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A376I7P4
#54: Protein 30S ribosomal protein S19


Mass: 10586.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: S1EA57
#55: Protein 30S ribosomal protein S20 / Small ribosomal subunit protein bS20


Mass: 9690.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7
#56: Protein 30S ribosomal protein S21 / Small ribosomal subunit protein bS21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68679
#57: Protein 30S ribosomal protein S1


Mass: 61224.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A829CYC5

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Protein , 1 types, 1 molecules v

#59: Protein UPF0115 protein YfcN


Mass: 20841.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: yfcN, mutS2, smrB, smrB_1, smrB_2, A5U30_004390, A8499_001840, A9819_13690, A9X72_07680, ABE90_016875, ACN68_23030, ACN81_17810, ACU57_26745, AT845_000599, AWP93_07555, BANRA_00899, BANRA_ ...Gene: yfcN, mutS2, smrB, smrB_1, smrB_2, A5U30_004390, A8499_001840, A9819_13690, A9X72_07680, ABE90_016875, ACN68_23030, ACN81_17810, ACU57_26745, AT845_000599, AWP93_07555, BANRA_00899, BANRA_03120, BANRA_03372, BF481_001004, BG944_000572, BGZ_01188, BGZ_03662, BHS81_14420, BIZ41_10480, BJI68_12470, BK292_05530, BMT49_14945, BN17_16361, BO068_000573, BOB65_001429, BOH76_07895, BON63_04725, BON64_17650, BON65_13895, BON66_23670, BON67_14425, BON68_20955, BON70_19955, BON72_07945, BON73_17545, BON74_06335, BON75_03320, BON76_16635, BON77_02335, BON78_04290, BON79_05115, BON80_19510, BON84_07205, BON88_15485, BON89_17570, BON90_11325, BON93_24455, BON94_16970, BON95_09375, BON97_08585, BON98_08660, BR158_002903, BSR05_08700, BTQ06_04170, BvCmsF30A_00313, BvCmsHHP019_01505, BvCmsHHP019_04741, BvCmsHHP056_04467, BvCmsKKP061_01272, BvCmsKSNP073_04721, BvCmsNSP072_04545, BVL39_15455, C2121_000219, C2U48_22750, C5N07_03940, C5Y87_03970, C9114_16420, C9160_05935, CCS08_07685, CCV12_002627, CDC27_12170, CG692_16040, CG831_000106, CIG67_19185, CQB02_04630, CR538_08010, CT143_04915, CV83915_03834, CWS33_01470, D3G36_02825, D9D77_18555, D9H94_01080, D9J61_20205, DAH18_01290, DAH19_01275, DAH20_01625, DAH22_02175, DAH27_09560, DAH28_11500, DAH29_05910, DAH30_16955, DAH31_06915, DAH32_12865, DAH34_11100, DAH35_01300, DAH36_15590, DAH37_19730, DAH41_07365, DAH50_05250, DEN88_00035, DEN89_08320, DEN90_05265, DEN91_02555, DEN92_02065, DEN93_02685, DEN94_01290, DEN95_01315, DEN96_01750, DEN97_01415, DEN98_01420, DEN99_05995, DEO00_00270, DEO01_17030, DEO02_01830, DEO03_03920, DEO04_00005, DEO05_00005, DEO06_08185, DEO07_00005, DEO08_00005, DEO09_00005, DEO10_00005, DEO11_00005, DEO12_00005, DEO13_01820, DEO14_01755, DEO15_01085, DEO17_01750, DEO18_04800, DEO19_01300, DEO20_01795, DIV22_21330, DN627_21615, DNQ45_19055, DRW19_09740, DS732_17835, DTL90_12855, DTM16_09590, DXT69_04490, DXT70_01870, DXT71_03185, E2112_03655, E2113_09810, E2117_01065, E2119_16395, E2121_01160, E2134_04330, E3N34_02270, E5P23_02715, E5P24_14725, E5P25_01670, E5P30_14800, E5P31_09445, E5P32_05070, E5P33_05410, E5P35_06605, E5P36_01995, E5P37_00385, E5P39_08050, E5P40_09805, E5P41_10890, E5P42_00250, E5P43_12380, E5P44_13535, E5P45_12690, E5P46_02815, E5P47_11675, E5P48_09480, E5P49_00460, E5P50_14395, E5P51_21390, E5S35_19735, E5S36_02955, E5S38_02620, E5S39_01460, E5S42_01695, E5S43_19350, E5S44_00375, E5S45_16565, E5S47_01205, E5S48_14270, E5S51_02300, E5S52_02190, E5S53_18875, E5S55_19065, E5S56_02640, E5S57_06985, EA239_07420, EA435_01595, EAN77_01305, EAX79_20205, EC1094V2_1345, EC3234A_175c01110, EC95NR1_01492, ED648_12345, EHD79_00295, EHH55_04655, EI021_18035, EIZ93_06290, EKI52_23470, ELT16_18350, ELT20_15195, ELT24_01425, ELT26_03990, ELT30_01440, ELT32_01920, ELT34_02590, ELT35_07845, ELT36_06875, ELT39_20410, ELT40_03580, ELT44_07815, ELT45_01435, ELT46_01450, ELT48_05880, ELT54_16840, ELT55_13610, ELT59_03260, ELT60_09215, ELT61_19220, ELT63_16105, ELT72_01435, ELU07_15110, ELU82_03765, ELU88_16655, ELU89_04385, ELU91_15800, ELU94_18550, ELU96_02215, ELU97_18185, ELU98_09905, ELV00_03615, ELV01_12085, ELV03_05730, ELV04_06410, ELV05_03280, ELV07_11430, ELV11_03535, ELV12_11720, ELV13_16905, ELV22_00040, ELV23_22840, ELV24_07090, ELV29_06140, ELX56_00135, ELX68_00090, ELX70_01865, ELX79_14975, ELX83_13520, ELX85_05845, ELY02_00645, ELY05_05535, ELY23_09510, ELY24_08500, ELY31_00705, ELY50_09115, ERS085406_02073, ERS139208_00454, EYV17_01290, EYV18_11375, F0L67_02300, F2N31_09430, F7F11_19875, F9V24_13620, F9X20_21990, FDM60_03010, FE587_23440, FEJ01_05060, FEL34_15690, FOI11_001300, FOI11_18750, FQ007_23030, FQF29_20000, FTV90_21245, FV293_07005, G3565_01615, G9448_22280, GF699_03390, GFY34_16620, GIB53_14855, GKF86_02695, GKF89_15515, GKG12_06190, GNZ05_23665, GP650_07760, GP662_01570, GP711_04770, GP946_05950, GQA06_05730, GQE64_02945, GQM09_01760, GQM13_01410, GQW07_19785, GRC73_01145, GRO95_21555, GRW57_06930, GRW81_01820, GUB92_01975, GUI33_05790, H0O53_19725, H0O72_00040, H6Y26_004289, HI055_002425, HIE29_002473, HIN64_001808, HKA49_003965, HLZ50_13880, HmCms169_00759, HMU06_04960, HMV41_01130, HV109_07165, HV146_16035, HV209_11120, HVV39_03830, HVX32_14355, HVY77_08085, HVZ29_14235, HX136_07310, I6H02_06990, IAI11_22020, IFB95_000286, IH772_06500, J0541_000123, J5U05_001006, JE86ST02C_27550, JE86ST05C_28400, JFD_00470, JNP96_19200, NCTC10089_01526, NCTC10767_02776, NCTC10865_01974, NCTC11181_03768, NCTC13148_02067, NCTC13216_05049, NCTC7928_01110, NCTC8008_00929, NCTC8009_02822, NCTC8179_04654, NCTC8333_01761, NCTC8450_03992, NCTC8621_01639, NCTC8622_03767, NCTC8960_04324, NCTC9001_01891, NCTC9036_01593, NCTC9045_01822, NCTC9073_04248, NCTC9111_01754, NCTC9775_05405, ND22_002524, PGD_00891, RG28_10175, SAMEA3472044_01606, SAMEA3472056_00624, SAMEA3472067_00013, SAMEA3472080_03598, SAMEA3751407_01308, SAMEA3752557_00674, WR15_08435
Production host: Escherichia coli (E. coli) / References: UniProt: Q6KCY1

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Non-polymers , 3 types, 12 molecules

#60: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#61: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#62: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: collided ribosome of the SmrB-bound disome structure / Type: RIBOSOME / Entity ID: #1-#59 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 42.4 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32412 / Symmetry type: POINT

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