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- PDB-6htq: Stringent response control by a bifunctional RelA enzyme in the p... -

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Basic information

Entry
Database: PDB / ID: 6htq
TitleStringent response control by a bifunctional RelA enzyme in the presence and absence of the ribosome
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 27
  • 16S rRNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • A/R-tRNA
  • E-tRNA
  • GTP pyrophosphokinase
  • P-tRNA
KeywordsRIBOSOME / Structure of bifunctional Rel on B. subtilis 70S
Function / homology
Function and homology information


GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / positive regulation of rRNA processing / nucleoid / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit ...GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / positive regulation of rRNA processing / nucleoid / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / kinase activity / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / phosphorylation / response to antibiotic / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
RelA/SpoT, AH and RIS domains / RelA/SpoT, AH and RIS domains / HD domain / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain ...RelA/SpoT, AH and RIS domains / RelA/SpoT, AH and RIS domains / HD domain / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / HD domain profile. / TGS domain profile. / TGS / TGS-like / HD domain / Ribosomal protein S14, type Z / Beta-grasp domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / 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 / Nucleotidyltransferase superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 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 L17 signature. / Ribosomal protein S14/S29 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / GTP pyrophosphokinase / Small ribosomal subunit protein uS11 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / GTP pyrophosphokinase / 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 / 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 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
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Bacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsWilson, D.N. / Abdelshahid, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Cell Rep / Year: 2020
Title: Structural Basis for Regulation of the Opposing (p)ppGpp Synthetase and Hydrolase within the Stringent Response Orchestrator Rel.
Authors: Patrick Pausch / Maha Abdelshahid / Wieland Steinchen / Heinrich Schäfer / Fabio Lino Gratani / Sven-Andreas Freibert / Christiane Wolz / Kürşad Turgay / Daniel N Wilson / Gert Bange /
Abstract: The stringent response enables metabolic adaptation of bacteria under stress conditions and is governed by RelA/SpoT Homolog (RSH)-type enzymes. Long RSH-type enzymes encompass an N-terminal domain ...The stringent response enables metabolic adaptation of bacteria under stress conditions and is governed by RelA/SpoT Homolog (RSH)-type enzymes. Long RSH-type enzymes encompass an N-terminal domain (NTD) harboring the second messenger nucleotide (p)ppGpp hydrolase and synthetase activity and a stress-perceiving and regulatory C-terminal domain (CTD). CTD-mediated binding of Rel to stalled ribosomes boosts (p)ppGpp synthesis. However, how the opposing activities of the NTD are controlled in the absence of stress was poorly understood. Here, we demonstrate on the RSH-type protein Rel that the critical regulative elements reside within the TGS (ThrRS, GTPase, and SpoT) subdomain of the CTD, which associates to and represses the synthetase to concomitantly allow for activation of the hydrolase. Furthermore, we show that Rel forms homodimers, which appear to control the interaction with deacylated-tRNA, but not the enzymatic activity of Rel. Collectively, our study provides a detailed molecular view into the mechanism of stringent response repression in the absence of stress.
History
DepositionOct 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 30, 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
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
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 L27
W: 50S ribosomal protein L28
X: 50S ribosomal protein L29
Y: 50S ribosomal protein L30
1: 50S ribosomal protein L32
2: 50S ribosomal protein L33 1
3: 50S ribosomal protein L34
4: 50S ribosomal protein L35
5: 50S ribosomal protein L36
Z: 50S ribosomal protein L31
a: 16S rRNA
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
v: P-tRNA
x: GTP pyrophosphokinase
u: A/R-tRNA
w: E-tRNA


Theoretical massNumber of molelcules
Total (without water)2,190,60953
Polymers2,190,60953
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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RNA chain , 6 types, 6 molecules ABavuw

#1: RNA chain 23S ribosomal RNA /


Mass: 948665.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1150402534
#2: RNA chain 5S ribosomal RNA /


Mass: 36157.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1150402534
#30: RNA chain 16S rRNA /


Mass: 496854.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 225184640
#50: RNA chain P-tRNA


Mass: 28094.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#52: RNA chain A/R-tRNA


Mass: 24486.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#53: RNA chain E-tRNA


Mass: 24140.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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50S ribosomal protein ... , 27 types, 27 molecules CDEFGJKLMNOPQRSTUVWXY12345Z

#3: Protein 50S ribosomal protein L2 / / BL2


Mass: 29674.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplB, BSU01190
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42919
#4: Protein 50S ribosomal protein L3 / / BL3


Mass: 22375.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplC, BSU01160
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42920
#5: Protein 50S ribosomal protein L4 /


Mass: 22222.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplD, BSU01170
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42921
#6: Protein 50S ribosomal protein L5 / / BL6


Mass: 19789.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplE, BSU01280
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12877
#7: Protein 50S ribosomal protein L6 / / BL10


Mass: 19124.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplF, BSU01310
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46898
#8: Protein 50S ribosomal protein L13 /


Mass: 16017.610 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplM, BSU01490
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P70974
#9: Protein 50S ribosomal protein L14 /


Mass: 13175.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplN, BSU01260
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12875
#10: Protein 50S ribosomal protein L15 /


Mass: 15410.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplO, BSU01350
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19946
#11: Protein 50S ribosomal protein L16 /


Mass: 15320.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplP, BSU01230
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P14577
#12: Protein 50S ribosomal protein L17 / / BL15 / BL21


Mass: 13643.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplQ, BSU01440
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20277
#13: Protein 50S ribosomal protein L18 / / BL16


Mass: 12993.829 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplR, BSU01320
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P46899
#14: Protein 50S ribosomal protein L19 /


Mass: 13416.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplS, BSU16040
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O31742
#15: Protein 50S ribosomal protein L20 /


Mass: 13408.813 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplT, BSU28850
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55873
#16: Protein 50S ribosomal protein L21 / / BL20


Mass: 11164.886 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplU, BSU27960
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P26908
#17: Protein 50S ribosomal protein L22 /


Mass: 12035.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplV, BSU01210
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42060
#18: Protein 50S ribosomal protein L23 /


Mass: 10387.095 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplW, BSU01180
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P42924
#19: Protein 50S ribosomal protein L24 / / 12 kDa DNA-binding protein / BL23 / HPB12


Mass: 10921.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rplX, BSU01270
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P0CI78
#20: Protein 50S ribosomal protein L27 / / BL24 / BL30


Mass: 8956.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpmA, BSU27940
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05657
#21: Protein 50S ribosomal protein L28 /


Mass: 6367.546 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpmB, yloT, BSU15820
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P37807
#22: Protein 50S ribosomal protein L29 /


Mass: 7598.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpmC, BSU01240
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12873
#23: Protein 50S ribosomal protein L30 / / BL27


Mass: 6519.599 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpmD, BSU01340
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P19947
#24: Protein 50S ribosomal protein L32 /


Mass: 6184.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpmF, BSU15080
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34687
#25: Protein/peptide 50S ribosomal protein L33 1 / Ribosome


Mass: 5786.696 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpmGA, rpmG1, BSU24900
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P56849
#26: Protein/peptide 50S ribosomal protein L34 /


Mass: 5271.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpmH, BSU41060
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P05647
#27: Protein 50S ribosomal protein L35 /


Mass: 7320.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpmI, BSU28860
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P55874
#28: 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 genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpmJ, BSU01400
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20278
#29: Protein 50S ribosomal protein L31 /


Mass: 7159.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpmE, BSU37070
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: Q03223

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

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


Mass: 25027.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsB, BSU16490
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21464
#32: Protein 30S ribosomal protein S3 / / BS3 / BS2


Mass: 23032.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsC, BSU01220
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21465
#33: Protein 30S ribosomal protein S4 / / BS4


Mass: 22250.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsD, BSU29660
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21466
#34: Protein 30S ribosomal protein S5 / / BS5


Mass: 17362.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsE, spcA, BSU01330
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21467
#35: Protein 30S ribosomal protein S6 / / BS9


Mass: 10723.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsF, BSU40910
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21468
#36: Protein 30S ribosomal protein S7 / / BS7


Mass: 16885.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsG, BSU01110
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21469
#37: Protein 30S ribosomal protein S8 / / BS8


Mass: 14770.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsH, BSU01300
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12879
#38: Protein 30S ribosomal protein S9 / / BS10


Mass: 13748.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsI, BSU01500
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21470
#39: Protein 30S ribosomal protein S10 / / BS13


Mass: 10856.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsJ, tetA, BSU01150
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21471
#40: Protein 30S ribosomal protein S11 / / BS11


Mass: 11946.558 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsK, BSU01420
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P04969
#41: Protein 30S ribosomal protein S12 / / BS12


Mass: 14988.358 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsL, fun, strA, BSU01100
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21472
#42: Protein 30S ribosomal protein S13 / / BS14


Mass: 12374.300 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsM, BSU01410
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P20282
#43: Protein 30S ribosomal protein S14 / / 30S ribosomal protein S14 type Z / 30S ribosomal protein S14-1 / BS-A


Mass: 7132.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsN1, rpsN, rpsNA, rpsZ, BSU01290
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12878
#44: Protein 30S ribosomal protein S15 / / BS18


Mass: 10124.599 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsO, BSU16680
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21473
#45: Protein 30S ribosomal protein S16 / / BS17


Mass: 9893.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsP, BSU15990
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21474
#46: Protein 30S ribosomal protein S17 / / BS16


Mass: 9863.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsQ, BSU01250
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P12874
#47: Protein 30S ribosomal protein S18 / / BS21


Mass: 7387.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsR, BSU40890
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21475
#48: Protein 30S ribosomal protein S19 / / BS19


Mass: 8990.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsS, BSU01200
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21476
#49: Protein 30S ribosomal protein S20 / / BS20


Mass: 9121.647 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rpsT, yqeO, BSU25550
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P21477

-
Protein , 1 types, 1 molecules x

#51: Protein GTP pyrophosphokinase / (p)ppGpp synthase / ATP:GTP 3'-pyrophosphotransferase / ppGpp synthase I


Mass: 39164.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: relA, BSU27600
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O54408, GTP diphosphokinase

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Experimental details

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Experiment

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

-
Sample preparation

ComponentName: Bacillus subtilis subsp. subtilis str. 168 / Type: RIBOSOME / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Source (recombinant)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Buffer solutionpH: 7.2
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 FIELDBright-field microscopy
Image recordingElectron dose: 2.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 650054 / Symmetry type: POINT

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