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- PDB-7o5b: Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-na... -

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Basic information

Entry
Database: PDB / ID: 7o5b
TitleCryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP bound
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 29
  • 16S rRNA (1533-MER)
  • 23S rRNA (2887-MER)
  • 5S rRNA (112-MER)
  • MifM-stalling construct
  • SRP RNA (266-MER)
  • Signal recognition particle protein
  • mRNA
  • tRNA
KeywordsRIBOSOME / signal recognition particle co-translational targeting alarmones translation GTPases stress response
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / positive regulation of rRNA processing / SRP-dependent cotranslational protein targeting to membrane / nucleoid / rRNA processing / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis ...signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / positive regulation of rRNA processing / SRP-dependent cotranslational protein targeting to membrane / nucleoid / rRNA processing / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / GTPase activity / mRNA binding / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Signal recognition particle protein / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain ...Signal recognition particle protein / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / : / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L17 signature. / 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 L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S14/S29 / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 ...GUANOSINE-5',3'-TETRAPHOSPHATE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL21 / Signal recognition particle protein / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsKratzat, H. / Czech, L. / Berninghausen, O. / Bange, G. / Beckmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)TRR174 Germany
CitationJournal: Nat Commun / Year: 2022
Title: Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp.
Authors: Laura Czech / Christopher-Nils Mais / Hanna Kratzat / Pinku Sarmah / Pietro Giammarinaro / Sven-Andreas Freibert / Hanna Folke Esser / Joanna Musial / Otto Berninghausen / Wieland Steinchen ...Authors: Laura Czech / Christopher-Nils Mais / Hanna Kratzat / Pinku Sarmah / Pietro Giammarinaro / Sven-Andreas Freibert / Hanna Folke Esser / Joanna Musial / Otto Berninghausen / Wieland Steinchen / Roland Beckmann / Hans-Georg Koch / Gert Bange /
Abstract: The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known ...The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known as (p)ppGpp. Here, we report that (p)ppGpp inhibits the signal recognition particle (SRP)-dependent protein targeting pathway, which is essential for membrane protein biogenesis and protein secretion. More specifically, (p)ppGpp binds to the SRP GTPases Ffh and FtsY, and inhibits the formation of the SRP receptor-targeting complex, which is central for the coordinated binding of the translating ribosome to the SecYEG translocon. Cryo-EM analysis of SRP bound to translating ribosomes suggests that (p)ppGpp may induce a distinct conformational stabilization of the NG domain of Ffh and FtsY in Bacillus subtilis but not in E. coli.
History
DepositionApr 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
U: tRNA
V: mRNA
W: SRP RNA (266-MER)
g: Signal recognition particle protein
h: MifM-stalling construct
p: 50S ribosomal protein L10
q: 50S ribosomal protein L11
X: 23S rRNA (2887-MER)
Y: 5S rRNA (112-MER)
Z: 50S ribosomal protein L2
a: 50S ribosomal protein L3
b: 50S ribosomal protein L4
c: 50S ribosomal protein L5
d: 50S ribosomal protein L6
e: 50S ribosomal protein L13
f: 50S ribosomal protein L14
i: 50S ribosomal protein L15
j: 50S ribosomal protein L16
k: 50S ribosomal protein L17
l: 50S ribosomal protein L18
m: 50S ribosomal protein L19
n: 50S ribosomal protein L20
o: 50S ribosomal protein L21
r: 50S ribosomal protein L22
s: 50S ribosomal protein L23
t: 50S ribosomal protein L24
u: 50S ribosomal protein L27
v: 50S ribosomal protein L28
w: 50S ribosomal protein L29
x: 50S ribosomal protein L30
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33 1
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
6: 50S ribosomal protein L31
A: 16S rRNA (1533-MER)
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,295,47557
Polymers2,294,87256
Non-polymers6031
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area244990 Å2
ΔGint-2053 kcal/mol
Surface area850030 Å2
MethodPISA

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Components

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RNA chain , 6 types, 6 molecules UVWXYA

#1: RNA chain tRNA


Mass: 24815.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1837880844
#2: RNA chain mRNA


Mass: 2612.665 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#3: RNA chain SRP RNA (266-MER)


Mass: 85909.688 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1837880844
#8: RNA chain 23S rRNA (2887-MER)


Mass: 936486.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1491848961
#9: RNA chain 5S rRNA (112-MER)


Mass: 36157.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1150402534
#37: RNA chain 16S rRNA (1533-MER)


Mass: 496854.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 225184640

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Protein , 2 types, 2 molecules gh

#4: Protein Signal recognition particle protein / Fifty-four homolog


Mass: 49739.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: ffh, BSU15980 / Production host: Escherichia coli (E. coli) / References: UniProt: P37105
#5: Protein MifM-stalling construct


Mass: 10874.593 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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50S ribosomal protein ... , 29 types, 29 molecules pqZabcdefijklmnorstuvwx012346

#6: Protein 50S ribosomal protein L10 / BL5 / Cold acclimatization protein / CAP / Vegetative protein 300 / VEG300


Mass: 18131.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42923
#7: Protein 50S ribosomal protein L11 / BL11


Mass: 14951.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q06796
#10: Protein 50S ribosomal protein L2 / BL2


Mass: 30335.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42919
#11: Protein 50S ribosomal protein L3 / BL3


Mass: 22594.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42920
#12: Protein 50S ribosomal protein L4


Mass: 22424.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42921
#13: Protein 50S ribosomal protein L5 / BL6


Mass: 20177.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12877
#14: Protein 50S ribosomal protein L6 / BL10


Mass: 19543.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46898
#15: Protein 50S ribosomal protein L13


Mass: 16407.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P70974
#16: Protein 50S ribosomal protein L14


Mass: 13175.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12875
#17: Protein 50S ribosomal protein L15


Mass: 15410.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19946
#18: Protein 50S ribosomal protein L16


Mass: 16223.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P14577
#19: Protein 50S ribosomal protein L17 / BL15 / BL21


Mass: 13774.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20277
#20: Protein 50S ribosomal protein L18 / BL16


Mass: 12993.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46899
#21: Protein 50S ribosomal protein L19


Mass: 13416.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O31742
#22: Protein 50S ribosomal protein L20


Mass: 13669.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55873
#23: Protein 50S ribosomal protein L21 / BL20


Mass: 11296.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P26908
#24: Protein 50S ribosomal protein L22


Mass: 12481.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42060
#25: Protein 50S ribosomal protein L23


Mass: 10978.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42924
#26: Protein 50S ribosomal protein L24 / 12 kDa DNA-binding protein / BL23 / HPB12


Mass: 11166.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P0CI78
#27: Protein 50S ribosomal protein L27 / BL24 / BL30


Mass: 10391.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05657
#28: Protein 50S ribosomal protein L28


Mass: 6826.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P37807
#29: Protein 50S ribosomal protein L29


Mass: 7728.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12873
#30: Protein 50S ribosomal protein L30 / BL27


Mass: 6650.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19947
#31: Protein 50S ribosomal protein L32


Mass: 6745.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34687
#32: Protein/peptide 50S ribosomal protein L33 1


Mass: 5915.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P56849
#33: Protein/peptide 50S ribosomal protein L34


Mass: 5271.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05647
#34: Protein 50S ribosomal protein L35


Mass: 7581.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55874
#35: Protein/peptide 50S ribosomal protein L36 / BL38 / Ribosomal protein B / Ribosomal protein II


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20278
#36: Protein 50S ribosomal protein L31


Mass: 7458.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q03223

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

#38: Protein 30S ribosomal protein S2 / BS1 / Vegetative protein 209 / VEG209


Mass: 28009.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21464
#39: Protein 30S ribosomal protein S3 / BS3 / BS2


Mass: 24351.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21465
#40: Protein 30S ribosomal protein S4 / BS4


Mass: 22874.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21466
#41: Protein 30S ribosomal protein S5 / BS5


Mass: 17650.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21467
#42: Protein 30S ribosomal protein S6 / BS9


Mass: 11140.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21468
#43: Protein 30S ribosomal protein S7 / BS7


Mass: 17915.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21469
#44: Protein 30S ribosomal protein S8 / BS8


Mass: 14901.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12879
#45: Protein 30S ribosomal protein S9 / BS10


Mass: 14335.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21470
#46: Protein 30S ribosomal protein S10 / BS13


Mass: 11687.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21471
#47: Protein 30S ribosomal protein S11 / BS11


Mass: 13993.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P04969
#48: Protein 30S ribosomal protein S12 / BS12


Mass: 15248.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21472
#49: Protein 30S ribosomal protein S13 / BS14


Mass: 13818.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20282
#50: Protein 30S ribosomal protein S14 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S14-1 / BS-A


Mass: 7263.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12878
#51: Protein 30S ribosomal protein S15 / BS18


Mass: 10597.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21473
#52: Protein 30S ribosomal protein S16 / BS17


Mass: 10153.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21474
#53: Protein 30S ribosomal protein S17 / BS16


Mass: 10220.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12874
#54: Protein 30S ribosomal protein S18 / BS21


Mass: 8990.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21475
#55: Protein 30S ribosomal protein S19 / BS19


Mass: 10607.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21476
#56: Protein 30S ribosomal protein S20 / BS20


Mass: 9622.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21477

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Non-polymers , 1 types, 1 molecules

#57: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4

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Details

Has ligand of interestN
Has protein modificationY

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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: SRP-bound MifM-stalled ribosome nascent chain complex / Type: RIBOSOME / Entity ID: #1-#56 / Source: MULTIPLE SOURCES
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
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21229 / Symmetry type: POINT

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