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- PDB-8v9l: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in ... -

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Basic information

Entry
Database: PDB / ID: 8v9l
TitleCryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Composite structure 6)
Components
  • (30S Ribosomal Protein ...) x 15
  • (50S ribosomal protein ...) x 20
  • (Large ribosomal subunit protein ...) x 12
  • (Small ribosomal subunit protein ...) x 5
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • Elongation factor TuEF-Tu
  • Ribosome hibernation factor Balon (MSMEG_1130)
  • pe/E deacylated phenylanaline-tRNA
  • poly-U mRNA
KeywordsRIBOSOME / cryo-EM / mycobacteria / hibernation / Msmeg1130 / Balon / MsmegEF-Tu
Function / homology
Function and homology information


translation elongation factor activity / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome ...translation elongation factor activity / large ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / GTPase activity / GTP binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Bacterial archaeo-eukaryotic release factor family 10 / Bacterial archaeo-eukaryotic release factor family 10 / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. ...Bacterial archaeo-eukaryotic release factor family 10 / Bacterial archaeo-eukaryotic release factor family 10 / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 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 / : / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S14, type Z / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / 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 L11, N-terminal / Ribosomal protein L17 signature. / 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/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, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / 50S ribosomal protein L30e-like / 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 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 L9/RNase H1, N-terminal / 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
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Peptide chain release factor 1 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 ...GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Peptide chain release factor 1 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Elongation factor Tu / Small ribosomal subunit protein uS10 / 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 uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / 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 bL31 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein bS18B / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL28
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsRybak, M.Y. / Helena-Bueno, K. / Hill, C.H. / Melnikov, S.V. / Gagnon, M.G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM136936 United States
Welch FoundationH-2032-20230405 United States
Other governmentJames W. McLaughlin Postdoctoral Fellowship
CitationJournal: Nature / Year: 2024
Title: A new family of bacterial ribosome hibernation factors.
Authors: Karla Helena-Bueno / Mariia Yu Rybak / Chinenye L Ekemezie / Rudi Sullivan / Charlotte R Brown / Charlotte Dingwall / Arnaud Baslé / Claudia Schneider / James P R Connolly / James N Blaza / ...Authors: Karla Helena-Bueno / Mariia Yu Rybak / Chinenye L Ekemezie / Rudi Sullivan / Charlotte R Brown / Charlotte Dingwall / Arnaud Baslé / Claudia Schneider / James P R Connolly / James N Blaza / Bálint Csörgő / Patrick J Moynihan / Matthieu G Gagnon / Chris H Hill / Sergey V Melnikov /
Abstract: To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of ...To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation.
History
DepositionDec 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
a: 16S Ribosomal RNA
b: 30S Ribosomal Protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: Small ribosomal subunit protein uS5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: Small ribosomal subunit protein uS8
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: Small ribosomal subunit protein uS14B
o: Small ribosomal subunit protein uS15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: Small ribosomal subunit protein bS18B
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20
u: 30S Ribosomal Protein S22
v: poly-U mRNA
x: Elongation factor Tu
y: pe/E deacylated phenylanaline-tRNA
z: Ribosome hibernation factor Balon (MSMEG_1130)
A: 23S Ribosomal RNA
B: 5S Ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: Large ribosomal subunit protein uL4
F: Large ribosomal subunit protein uL5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
I: 50S ribosomal protein L10
J: 50S ribosomal protein L11
L: Large ribosomal subunit protein uL13
M: 50S ribosomal protein L14
N: 50S ribosomal protein L15
O: Large ribosomal subunit protein uL16
P: 50S ribosomal protein L17
Q: Large ribosomal subunit protein uL18
R: 50S ribosomal protein L19
S: Large ribosomal subunit protein bL20
T: Large ribosomal subunit protein bL21
U: Large ribosomal subunit protein uL22
V: Large ribosomal subunit protein uL23
W: 50S ribosomal protein L24
X: 50S ribosomal protein L25
Y: 50S ribosomal protein L27
Z: Large ribosomal subunit protein bL28
1: 50S ribosomal protein L29
2: 50S ribosomal protein L30
3: Large ribosomal subunit protein bL31
4: 50S ribosomal protein L32
5: Large ribosomal subunit protein bL33A
6: 50S ribosomal protein L34
7: 50S ribosomal protein L35
8: 50S ribosomal protein L36
9: 50S Ribosomal Protein L27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,405,64362
Polymers2,405,06959
Non-polymers5743
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 5 types, 5 molecules avyAB

#1: RNA chain 16S Ribosomal RNA /


Mass: 495373.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: GenBank: 118168627
#22: RNA chain poly-U mRNA


Mass: 1179.706 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155
#24: RNA chain pe/E deacylated phenylanaline-tRNA


Mass: 24531.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155
#26: RNA chain 23S Ribosomal RNA /


Mass: 1026283.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: GenBank: 118168627
#27: RNA chain 5S Ribosomal RNA /


Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: GenBank: 118168627

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30S Ribosomal Protein ... , 15 types, 15 molecules bcdfgijklmpqstu

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


Mass: 30145.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QVB8
#3: Protein 30S ribosomal protein S3 /


Mass: 30191.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSD7
#4: Protein 30S ribosomal protein S4 /


Mass: 23415.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSL7
#6: 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)
Strain: MC2155 / References: UniProt: A0A2U9Q0X2
#7: Protein 30S ribosomal protein S7 /


Mass: 17660.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QS97
#9: Protein 30S ribosomal protein S9 /


Mass: 16794.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSP9
#10: Protein 30S ribosomal protein S10 /


Mass: 11454.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSD0
#11: Protein 30S ribosomal protein S11 /


Mass: 14671.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSL6
#12: Protein 30S ribosomal protein S12 /


Mass: 13896.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QS96
#13: Protein 30S ribosomal protein S13 /


Mass: 14249.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSL5
#16: Protein 30S ribosomal protein S16 /


Mass: 16795.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QV37
#17: Protein 30S ribosomal protein S17 /


Mass: 11127.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSE0
#19: Protein 30S ribosomal protein S19 /


Mass: 10800.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSD5
#20: Protein 30S ribosomal protein S20 /


Mass: 9556.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0R102
#21: Protein/peptide 30S Ribosomal Protein S22 /


Mass: 4164.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155

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Small ribosomal subunit protein ... , 5 types, 5 molecules ehnor

#5: Protein Small ribosomal subunit protein uS5


Mass: 21946.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSG6
#8: Protein Small ribosomal subunit protein uS8


Mass: 14492.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSG3
#14: Protein Small ribosomal subunit protein uS14B


Mass: 6976.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSG2
#15: Protein Small ribosomal subunit protein uS15


Mass: 10368.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QVQ3
#18: Protein Small ribosomal subunit protein bS18B


Mass: 9524.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0R7F7

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Protein , 2 types, 2 molecules xz

#23: Protein Elongation factor Tu / EF-Tu


Mass: 43792.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MsmegEF-Tu
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / Gene: tuf / Plasmid: pET28-SMT3-MsmegEF-Tu / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QS98
#25: Protein Ribosome hibernation factor Balon (MSMEG_1130)


Mass: 41390.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MSMEG_1130
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / Gene: MSMEG_1130 / Plasmid: pET28-SMT3-MSMEG_1130 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QRI6

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50S ribosomal protein ... , 20 types, 20 molecules CDGHIJMNPRWXY1246789

#28: Protein 50S ribosomal protein L2 /


Mass: 30425.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSD4
#29: Protein 50S ribosomal protein L3 /


Mass: 23011.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSD1
#32: Protein 50S ribosomal protein L6 /


Mass: 19483.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSG4
#33: 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)
Strain: MC2155 / References: UniProt: A0R7F6
#34: Protein 50S ribosomal protein L10 /


Mass: 18035.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QS62
#35: Protein 50S ribosomal protein L11 /


Mass: 15023.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QS45
#37: 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)
Strain: MC2155 / References: UniProt: A0QSF9
#38: Protein 50S ribosomal protein L15 /


Mass: 15602.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSG8
#40: Protein 50S ribosomal protein L17 /


Mass: 21892.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSL9
#42: 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)
Strain: MC2155 / References: UniProt: A0QV42
#47: 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)
Strain: MC2155 / References: UniProt: A0QSG0
#48: Protein 50S ribosomal protein L25 / / General stress protein CTC


Mass: 22571.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0R3D2
#49: Protein 50S ribosomal protein L27 /


Mass: 9249.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0R150
#51: Protein 50S ribosomal protein L29 /


Mass: 8790.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSD9
#52: Protein 50S ribosomal protein L30 /


Mass: 7022.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSG7
#54: Protein 50S ribosomal protein L32 /


Mass: 6467.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0R3I9
#56: Protein/peptide 50S ribosomal protein L34 /


Mass: 5522.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0R7K0
#57: Protein 50S ribosomal protein L35 /


Mass: 7298.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QYU7
#58: 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)
Strain: MC2155 / References: UniProt: A0QSL4
#59: Protein/peptide 50S Ribosomal Protein L27 /


Mass: 2841.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QTP4

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Large ribosomal subunit protein ... , 12 types, 12 molecules EFLOQSTUVZ35

#30: Protein Large ribosomal subunit protein uL4


Mass: 22920.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSD2
#31: Protein Large ribosomal subunit protein uL5


Mass: 21152.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSG1
#36: Protein Large ribosomal subunit protein uL13


Mass: 16146.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSP8
#39: Protein Large ribosomal subunit protein uL16


Mass: 15627.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSD8
#41: Protein Large ribosomal subunit protein uL18


Mass: 13711.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: I7FGD9
#43: Protein Large ribosomal subunit protein bL20


Mass: 14494.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QYU6
#44: Protein Large ribosomal subunit protein bL21


Mass: 11055.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0R151
#45: Protein Large ribosomal subunit protein uL22


Mass: 16353.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSD6
#46: Protein Large ribosomal subunit protein uL23


Mass: 11047.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QSD3
#50: Protein Large ribosomal subunit protein bL28


Mass: 6891.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: I7FJ52
#53: Protein Large ribosomal subunit protein bL31


Mass: 8312.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0R215
#55: Protein Large ribosomal subunit protein bL33A


Mass: 6468.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2155 / References: UniProt: A0QS39

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Non-polymers , 2 types, 3 molecules

#60: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#61: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Composite structure 6)
Type: RIBOSOME / Entity ID: #1-#59 / Source: NATURAL
Molecular weightValue: 2.6 MDa / Experimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 7.5
Details: 20 mM HEPES-KOH, 60 mM KCl, 10 mM MgCl2, 1 mM dithiothreitol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40.12 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10161

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2SerialEMimage acquisition
3cryoSPARC4.2.1masking
4cryoSPARC4.2.1CTF correction
7UCSF Chimera1.14model fitting
9PHENIX1.19.2.4158model refinement
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
12cryoSPARC4.2.1classification
13cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101909 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 5o61

5o61


Accession code: 5o61 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006168692
ELECTRON MICROSCOPYf_angle_d0.673251706
ELECTRON MICROSCOPYf_dihedral_angle_d14.66864940
ELECTRON MICROSCOPYf_chiral_restr0.04232085
ELECTRON MICROSCOPYf_plane_restr0.00614228

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