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- PDB-6h58: Structure of a hibernating 100S ribosome reveals an inactive conf... -

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Basic information

Entry
Database: PDB / ID: 6h58
TitleStructure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome
Components
  • (30S ribosomal protein ...) x 21
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Ribosome hibernation promoting factor
  • Ribosome modulation factor
  • tRNA Mixture
KeywordsRIBOSOME / 100S / cryo-EM / E-site tRNA / hibernation / HPF / RMF / S1
Function / homology
Function and homology information


dormancy process / negative regulation of translation in response to stress / negative regulation of translational elongation / positive regulation of cytoplasmic translation / cellular response to stress / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / ribosomal small subunit binding / misfolded RNA binding ...dormancy process / negative regulation of translation in response to stress / negative regulation of translational elongation / positive regulation of cytoplasmic translation / cellular response to stress / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / ribosomal small subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / regulation of mRNA stability / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / response to reactive oxygen species / ribosome assembly / transcription elongation factor complex / DNA endonuclease activity / transcription antitermination / regulation of cell growth / translational initiation / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / large ribosomal subunit / ribosome biogenesis / ribosome binding / 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 / single-stranded RNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Ribosome modulation factor / Ribosome modulation factor domain superfamily / Ribosome modulation factor / : / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein S1 / Ribosomal protein S1-like ...Ribosome modulation factor / Ribosome modulation factor domain superfamily / Ribosome modulation factor / : / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein S1 / Ribosomal protein S1-like / S1 domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / Ribosomal protein L31 type A / S1 RNA binding domain / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 / 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 S21 / 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 L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / 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 / Ribosomal protein L9, N-terminal domain superfamily / 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 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Ribosome modulation factor / Ribosome hibernation promoting factor / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS1 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsBeckert, B. / Turk, M. / Czech, A. / Berninghausen, O. / Beckmann, R. / Ignatova, Z. / Plitzko, J. / Wilson, D.N.
Funding support Germany, 2items
OrganizationGrant numberCountry
SPP1879 Germany
FOR1805 Germany
CitationJournal: Nat Microbiol / Year: 2018
Title: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1.
Authors: Bertrand Beckert / Martin Turk / Andreas Czech / Otto Berninghausen / Roland Beckmann / Zoya Ignatova / Jürgen M Plitzko / Daniel N Wilson /
Abstract: To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles. In γ-proteobacteria, such as Escherichia coli, 100S ...To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles. In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF). Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria, and reveals a unique role for bS1 in translation regulation.
History
DepositionJul 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
0: 50S ribosomal protein L32
1: 50S ribosomal protein L33
2: 50S ribosomal protein L34
3: 50S ribosomal protein L35
4: 50S ribosomal protein L36
6: 50S ribosomal protein L31
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
H: 50S ribosomal protein L9
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 L25
W: 50S ribosomal protein L27
X: 50S ribosomal protein L28
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
a: 16S ribosomal RNA
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
u: 30S ribosomal protein S21
v: Ribosome modulation factor
x: Ribosome hibernation promoting factor
y: 30S ribosomal protein S1
w: tRNA Mixture
00: 50S ribosomal protein L32
11: 50S ribosomal protein L33
22: 50S ribosomal protein L34
33: 50S ribosomal protein L35
44: 50S ribosomal protein L36
66: 50S ribosomal protein L31
AA: 23S ribosomal RNA
BB: 5S ribosomal RNA
CC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
EE: 50S ribosomal protein L4
FF: 50S ribosomal protein L5
GG: 50S ribosomal protein L6
HH: 50S ribosomal protein L9
JJ: 50S ribosomal protein L13
KK: 50S ribosomal protein L14
LL: 50S ribosomal protein L15
MM: 50S ribosomal protein L16
NN: 50S ribosomal protein L17
OO: 50S ribosomal protein L18
PP: 50S ribosomal protein L19
QQ: 50S ribosomal protein L20
RR: 50S ribosomal protein L21
SS: 50S ribosomal protein L22
TT: 50S ribosomal protein L23
UU: 50S ribosomal protein L24
VV: 50S ribosomal protein L25
WW: 50S ribosomal protein L27
XX: 50S ribosomal protein L28
YY: 50S ribosomal protein L29
ZZ: 50S ribosomal protein L30
aa: 16S ribosomal RNA
bb: 30S ribosomal protein S2
cc: 30S ribosomal protein S3
dd: 30S ribosomal protein S4
ee: 30S ribosomal protein S5
ff: 30S ribosomal protein S6
gg: 30S ribosomal protein S7
hh: 30S ribosomal protein S8
ii: 30S ribosomal protein S9
jj: 30S ribosomal protein S10
kk: 30S ribosomal protein S11
ll: 30S ribosomal protein S12
mm: 30S ribosomal protein S13
nn: 30S ribosomal protein S14
oo: 30S ribosomal protein S15
pp: 30S ribosomal protein S16
qq: 30S ribosomal protein S17
rr: 30S ribosomal protein S18
ss: 30S ribosomal protein S19
tt: 30S ribosomal protein S20
uu: 30S ribosomal protein S21
vv: Ribosome modulation factor
xx: Ribosome hibernation promoting factor
yy: 30S ribosomal protein S1
ww: tRNA Mixture


Theoretical massNumber of molelcules
Total (without water)4,434,580112
Polymers4,434,580112
Non-polymers00
Water00
1


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

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Components

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50S ribosomal protein ... , 29 types, 58 molecules 000111222333444666CCCDDDEEEFFFGGGHHHJJJKKKLLL...

#1: Protein 50S ribosomal protein L32 / Large ribosomal subunit protein bL32


Mass: 6332.249 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7N4
#2: Protein/peptide 50S ribosomal protein L33 / Large ribosomal subunit protein bL33


Mass: 5814.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7N9
#3: Protein/peptide 50S ribosomal protein L34 / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7P5
#4: Protein 50S ribosomal protein L35 / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7Q1
#5: Protein/peptide 50S ribosomal protein L36 / Large ribosomal subunit protein bL36-A / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7Q6
#6: Protein 50S ribosomal protein L31 / Large ribosomal subunit protein bL31-A


Mass: 7516.693 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7M9
#9: Protein 50S ribosomal protein L2 / Large ribosomal subunit protein uL2


Mass: 29663.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P60422
#10: Protein 50S ribosomal protein L3 / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P60438
#11: Protein 50S ribosomal protein L4 / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P60723
#12: Protein 50S ribosomal protein L5 / Large ribosomal subunit protein uL5


Mass: 20073.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P62399
#13: Protein 50S ribosomal protein L6 / Large ribosomal subunit protein uL6


Mass: 18801.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG55
#14: Protein 50S ribosomal protein L9 / Large ribosomal subunit protein bL9


Mass: 15789.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7R1
#15: Protein 50S ribosomal protein L13 / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AA10
#16: Protein 50S ribosomal protein L14 / Large ribosomal subunit protein uL14


Mass: 13451.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0ADY3
#17: Protein 50S ribosomal protein L15 / Large ribosomal subunit protein uL15


Mass: 14877.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02413
#18: Protein 50S ribosomal protein L16 / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0ADY7
#19: Protein 50S ribosomal protein L17 / Large ribosomal subunit protein bL17


Mass: 13721.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG44
#20: Protein 50S ribosomal protein L18 / Large ribosomal subunit protein uL18


Mass: 12663.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0C018
#21: Protein 50S ribosomal protein L19 / Large ribosomal subunit protein bL19


Mass: 13028.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7K6
#22: Protein 50S ribosomal protein L20 / Large ribosomal subunit protein bL20


Mass: 13396.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7L3
#23: Protein 50S ribosomal protein L21 / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG48
#24: Protein 50S ribosomal protein L22 / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P61175
#25: Protein 50S ribosomal protein L23 / Large ribosomal subunit protein uL23


Mass: 10546.472 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0ADZ0
#26: Protein 50S ribosomal protein L24 / Large ribosomal subunit protein uL24


Mass: 11078.874 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P60624
#27: Protein 50S ribosomal protein L25 / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P68919
#28: Protein 50S ribosomal protein L27 / Large ribosomal subunit protein bL27


Mass: 8174.394 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7L8
#29: Protein 50S ribosomal protein L28 / Large ribosomal subunit protein bL28


Mass: 8896.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7M2
#30: Protein 50S ribosomal protein L29 / Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7M6
#31: Protein 50S ribosomal protein L30 / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG51

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RNA chain , 4 types, 8 molecules AAABBBaaawww

#7: RNA chain 23S ribosomal RNA


Mass: 941305.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1036415628
#8: RNA chain 5S ribosomal RNA


Mass: 38813.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1393501787
#32: RNA chain 16S ribosomal RNA


Mass: 498725.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1359176725
#56: RNA chain tRNA Mixture


Mass: 24771.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1063812051

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30S ribosomal protein ... , 21 types, 42 molecules bbbcccdddeeefffggghhhiiijjjkkklllmmmnnnoooppp...

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


Mass: 25096.799 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V0
#34: Protein 30S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 23078.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V3
#35: Protein 30S ribosomal protein S4 / Small ribosomal subunit protein uS4


Mass: 23383.002 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V8
#36: Protein 30S ribosomal protein S5 / Small ribosomal subunit protein uS5


Mass: 16532.088 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7W1
#37: Protein 30S ribosomal protein S6 / Small ribosomal subunit protein bS6


Mass: 11669.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02358
#38: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 18048.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02359
#39: Protein 30S ribosomal protein S8 / Small ribosomal subunit protein uS8


Mass: 14015.361 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7W7
#40: Protein 30S ribosomal protein S9 / Small ribosomal subunit protein uS9


Mass: 14554.882 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7X3
#41: Protein 30S ribosomal protein S10 / Small ribosomal subunit protein uS10


Mass: 11196.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7R5
#42: Protein 30S ribosomal protein S11 / Small ribosomal subunit protein uS11


Mass: 12388.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7R9
#43: Protein 30S ribosomal protein S12 / Small ribosomal subunit protein uS12


Mass: 13636.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7S3
#44: Protein 30S ribosomal protein S13 / Small ribosomal subunit protein uS13


Mass: 12625.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7S9
#45: Protein 30S ribosomal protein S14 / Small ribosomal subunit protein uS14


Mass: 11546.442 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG59
#46: Protein 30S ribosomal protein S15 / Small ribosomal subunit protein uS15


Mass: 10159.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0ADZ4
#47: Protein 30S ribosomal protein S16 / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7T3
#48: Protein 30S ribosomal protein S17 / Small ribosomal subunit protein uS17


Mass: 9263.946 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG63
#49: Protein 30S ribosomal protein S18 / Small ribosomal subunit protein bS18


Mass: 7606.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7T7
#50: Protein 30S ribosomal protein S19 / Small ribosomal subunit protein uS19


Mass: 9057.626 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7U3
#51: Protein 30S ribosomal protein S20 / Small ribosomal subunit protein bS20


Mass: 9506.190 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7U7
#52: Protein 30S ribosomal protein S21 / Small ribosomal subunit protein bS21


Mass: 7763.073 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P68679
#55: Protein 30S ribosomal protein S1 / Bacteriophage Q beta RNA-directed RNA polymerase subunit I / Small ribosomal subunit protein bS1


Mass: 61238.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG67

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Protein , 2 types, 4 molecules vvvxxx

#53: Protein Ribosome modulation factor / RMF / Hibernation factor RMF / Protein E


Mass: 6520.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AFW2
#54: Protein Ribosome hibernation promoting factor / HPF / Hibernation factor HPF


Mass: 10768.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AFX0

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1
Type: RIBOSOME
Details: single particle cryo-electron microscopy structures of hibernating 100S particles isolated from stationary phase E. coli cells
Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE-PROPANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 1.15 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
4GctfCTF correction
7UCSF Chimeramodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 6H4N

6h4n


Accession code: 6H4N / Source name: PDB / Type: experimental model

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