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- PDB-8fr8: Structure of Mycobacterium smegmatis Rsh bound to a 70S translati... -

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Basic information

Entry
Database: PDB / ID: 8fr8
TitleStructure of Mycobacterium smegmatis Rsh bound to a 70S translation initiation complex
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 32
  • 16S rRNA (1511-MER)
  • 23S rRNA (3119-MER)
  • 5S rRNA (118-MER)
  • GTP pyrophosphokinase RelA
  • fMet tRNA (77-MER)
  • mRNA
KeywordsTRANSLATION / starvation sensing / RelA/SpoT homologue / Mycobacterium / 70S initiation complex
Function / homology
Function and homology information


GTP diphosphokinase / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / kinase activity / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding ...GTP diphosphokinase / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / kinase activity / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / GTP binding / RNA binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RelA/SpoT, AH and RIS domains / RelA/SpoT, AH and RIS domains / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / HD domain / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain ...RelA/SpoT, AH and RIS domains / RelA/SpoT, AH and RIS domains / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / HD domain / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / Ribosomal protein L31 type B / ACT domain profile. / ACT domain / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / HD domain profile. / ACT-like domain / TGS-like / TGS domain profile. / TGS / HD domain / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / Beta-grasp domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Ribosomal protein L11, bacterial-type / Ribosomal protein S14, bacterial/plastid / Nucleotidyltransferase superfamily / 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 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 L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / 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 L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 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 L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / AURKAIP1/COX24 domain-containing protein / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL11 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / AURKAIP1/COX24 domain-containing protein / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Uncharacterized protein / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS18A / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein bL33B / Large ribosomal subunit protein bL28 / 50S ribosomal protein L31 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34 / GTP diphosphokinase / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL15
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsMajumdar, S. / Sharma, M.R. / Manjari, S.R. / Banavali, N.K. / Agrawal, R.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI132422 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM61576 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Starvation sensing by mycobacterial RelA/SpoT homologue through constitutive surveillance of translation.
Authors: Yunlong Li / Soneya Majumdar / Ryan Treen / Manjuli R Sharma / Jamie Corro / Howard B Gamper / Swati R Manjari / Jerome Prusa / Nilesh K Banavali / Christina L Stallings / Ya-Ming Hou / ...Authors: Yunlong Li / Soneya Majumdar / Ryan Treen / Manjuli R Sharma / Jamie Corro / Howard B Gamper / Swati R Manjari / Jerome Prusa / Nilesh K Banavali / Christina L Stallings / Ya-Ming Hou / Rajendra K Agrawal / Anil K Ojha /
Abstract: The stringent response, which leads to persistence of nutrient-starved mycobacteria, is induced by activation of the RelA/SpoT homolog (Rsh) upon entry of a deacylated-tRNA in a translating ribosome. ...The stringent response, which leads to persistence of nutrient-starved mycobacteria, is induced by activation of the RelA/SpoT homolog (Rsh) upon entry of a deacylated-tRNA in a translating ribosome. However, the mechanism by which Rsh identifies such ribosomes in vivo remains unclear. Here, we show that conditions inducing ribosome hibernation result in loss of intracellular Rsh in a Clp protease-dependent manner. This loss is also observed in nonstarved cells using mutations in Rsh that block its interaction with the ribosome, indicating that Rsh association with the ribosome is important for Rsh stability. The cryo-EM structure of the Rsh-bound 70S ribosome in a translation initiation complex reveals unknown interactions between the ACT domain of Rsh and components of the ribosomal L7/L12 stalk base, suggesting that the aminoacylation status of A-site tRNA is surveilled during the first cycle of elongation. Altogether, we propose a surveillance model of Rsh activation that originates from its constitutive interaction with the ribosomes entering the translation cycle.
History
DepositionJan 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
c: 50S ribosomal protein L33 2
y: 50S ribosomal protein L28
E: fMet tRNA (77-MER)
d: 30S ribosomal protein S19
B: 5S rRNA (118-MER)
j: 30S ribosomal protein S13
N: 50S ribosomal protein L16
3: 50S ribosomal protein eL31
A: 23S rRNA (3119-MER)
K: 50S ribosomal protein L2
L: 50S ribosomal protein L3
M: 50S ribosomal protein L4
O: 50S ribosomal protein L5
P: 50S ribosomal protein L6
Q: 50S ribosomal protein L9
R: 50S ribosomal protein L10
S: 50S ribosomal protein L11
T: 50S ribosomal protein L13
U: 50S ribosomal protein L14
V: 50S ribosomal protein L15
J: 50S ribosomal protein L17
D: 50S ribosomal protein L18
C: 50S ribosomal protein L19
W: 50S ribosomal protein L20
X: 50S ribosomal protein L21
Y: 50S ribosomal protein L22
Z: 50S ribosomal protein L23
1: 50S ribosomal protein L24
2: 50S ribosomal protein L25
4: 50S ribosomal protein L27
6: 50S ribosomal protein L29
7: 50S ribosomal protein L30
8: 50S ribosomal protein L32
0: 50S ribosomal protein L34
x: 50S ribosomal protein L35
F: 50S ribosomal protein L36
a: 16S rRNA (1511-MER)
b: 30S ribosomal protein S22
G: 30S ribosomal protein S3
e: 30S ribosomal protein S4
f: 30S ribosomal protein S5
g: 30S ribosomal protein S6
h: 30S ribosomal protein S7
i: 30S ribosomal protein S8
k: 30S ribosomal protein S9
l: 30S ribosomal protein S10
m: 30S ribosomal protein S11
n: 30S ribosomal protein S12
p: 30S ribosomal protein S15
q: 30S ribosomal protein S16
r: 30S ribosomal protein S17
t: 30S ribosomal protein S20
u: 30S ribosomal protein S2
v: mRNA
I: GTP pyrophosphokinase RelA
H: 50S ribosomal protein L31
o: 30S ribosomal protein S18 1
9: 30S ribosomal protein S14


Theoretical massNumber of molelcules
Total (without water)2,345,27858
Polymers2,345,27858
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 32 types, 32 molecules cyN3KLMOPQRSTUVJDCWXYZ1246780xFH

#1: Protein 50S ribosomal protein L33 2


Mass: 6484.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R551
#2: Protein 50S ribosomal protein L28


Mass: 8729.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R552
#7: Protein 50S ribosomal protein L16


Mass: 15498.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD8
#8: Protein/peptide 50S ribosomal protein eL31


Mass: 2710.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTP4
#10: Protein 50S ribosomal protein L2


Mass: 30008.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD4
#11: Protein 50S ribosomal protein L3


Mass: 22621.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD1
#12: Protein 50S ribosomal protein L4


Mass: 22346.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD2
#13: Protein 50S ribosomal protein L5


Mass: 20588.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG1
#14: Protein 50S ribosomal protein L6


Mass: 19165.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG4
#15: Protein 50S ribosomal protein L9


Mass: 15949.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R7F6
#16: Protein 50S ribosomal protein L10


Mass: 13095.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS62
#17: Protein 50S ribosomal protein L11


Mass: 14109.185 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS45
#18: Protein 50S ribosomal protein L13


Mass: 16015.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSP8
#19: Protein 50S ribosomal protein L14


Mass: 13400.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSF9
#20: Protein 50S ribosomal protein L15


Mass: 15383.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7G436
#21: Protein 50S ribosomal protein L17


Mass: 13210.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL9
#22: Protein 50S ribosomal protein L18


Mass: 13580.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7FGD9
#23: Protein 50S ribosomal protein L19


Mass: 12892.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QV42
#24: Protein 50S ribosomal protein L20


Mass: 14035.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QYU6
#25: Protein 50S ribosomal protein L21


Mass: 10724.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R151
#26: Protein 50S ribosomal protein L22


Mass: 12408.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD6
#27: Protein 50S ribosomal protein L23


Mass: 10748.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD3
#28: Protein 50S ribosomal protein L24


Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG0
#29: Protein 50S ribosomal protein L25


Mass: 20331.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R3D2
#30: Protein 50S ribosomal protein L27


Mass: 8322.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R150
#31: Protein 50S ribosomal protein L29


Mass: 7590.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD9
#32: Protein 50S ribosomal protein L30


Mass: 6761.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG7
#33: Protein 50S ribosomal protein L32


Mass: 6050.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R3I9
#34: Protein/peptide 50S ribosomal protein L34


Mass: 5391.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R7K0
#35: Protein 50S ribosomal protein L35


Mass: 7167.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QYU7
#36: Protein/peptide 50S ribosomal protein L36


Mass: 4341.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL4
#56: Protein 50S ribosomal protein L31


Mass: 9141.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R554

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RNA chain , 5 types, 5 molecules EBAav

#3: RNA chain fMet tRNA (77-MER)


Mass: 24780.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Production host: Escherichia coli (E. coli) / References: GenBank: 1329944645
#5: RNA chain 5S rRNA (118-MER)


Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: GenBank: 118168627
#9: RNA chain 23S rRNA (3119-MER)


Mass: 1011834.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: GenBank: 118168627
#37: RNA chain 16S rRNA (1511-MER)


Mass: 490111.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: GenBank: 118168627
#54: RNA chain mRNA


Mass: 6502.976 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycolicibacterium smegmatis MC2 155 (bacteria)

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30S ribosomal protein ... , 20 types, 20 molecules djbGefghiklmnpqrtuo9

#4: Protein 30S ribosomal protein S19


Mass: 9379.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD5
#6: Protein 30S ribosomal protein S13


Mass: 13374.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL5
#38: Protein/peptide 30S ribosomal protein S22 / AURKAIP1/COX24 domain-containing protein


Mass: 4033.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0A2G8BJD4
#39: Protein 30S ribosomal protein S3


Mass: 23617.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD7
#40: Protein 30S ribosomal protein S4


Mass: 23284.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL7
#41: Protein 30S ribosomal protein S5


Mass: 18481.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG6
#42: Protein 30S ribosomal protein S6


Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0A2U9Q0X2
#43: Protein 30S ribosomal protein S7


Mass: 17529.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS97
#44: Protein 30S ribosomal protein S8


Mass: 14361.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG3
#45: Protein 30S ribosomal protein S9


Mass: 14093.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSP9
#46: Protein 30S ribosomal protein S10


Mass: 11252.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0A7I7K4Z0
#47: Protein 30S ribosomal protein S11


Mass: 12151.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL6
#48: Protein 30S ribosomal protein S12


Mass: 13678.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS96
#49: Protein 30S ribosomal protein S15


Mass: 10236.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QVQ3
#50: Protein 30S ribosomal protein S16


Mass: 12635.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QV37
#51: Protein 30S ribosomal protein S17


Mass: 10680.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSE0
#52: Protein 30S ribosomal protein S20


Mass: 9424.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R102
#53: Protein 30S ribosomal protein S2


Mass: 25576.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QVB8
#57: Protein 30S ribosomal protein S18 1


Mass: 9449.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R549
#58: Protein 30S ribosomal protein S14


Mass: 11661.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R550

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Protein , 1 types, 1 molecules I

#55: Protein GTP pyrophosphokinase RelA


Mass: 88057.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: relA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: I7FCZ4

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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: Mycobacterium smegmatis 70S ribosome bound to Rsh, and initiator tRNA-fMet
Type: RIBOSOME / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 66.59 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4.0-beta-2particle selection
2Leginonimage acquisition
4CTFFIND4.1CTF correction
7Coot0.8.8 ELmodel fitting
10RELION4.0-beta-2final Euler assignment
11RELION4.0-beta-2classification
12RELION4.0-beta-23D reconstruction
13PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1928609
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36321 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005165983
ELECTRON MICROSCOPYf_angle_d0.611248351
ELECTRON MICROSCOPYf_dihedral_angle_d15.9165121
ELECTRON MICROSCOPYf_chiral_restr0.03731750
ELECTRON MICROSCOPYf_plane_restr0.00513531

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