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- PDB-28uk: E. coli 70S ribosome, conformational ground state mutation in SSU... -

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Basic information

Entry
Database: PDB / ID: 28uk
TitleE. coli 70S ribosome, conformational ground state mutation in SSU-h41, with A- and P-site tRNA
Components
  • (Large ribosomal subunit protein ...) x 29
  • (Small ribosomal subunit protein ...) x 20
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • A-site Val-tRNA^Val
  • P-site tRNA^fMet
  • mRNA
KeywordsRIBOSOME / 70S ribosome / RNA excited states
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / transcription antitermination factor activity, RNA binding / ornithine decarboxylase inhibitor activity / 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 translational initiation / transcription antitermination factor activity, RNA binding / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / four-way junction DNA binding / negative regulation of cytoplasmic translation / DnaA-L2 complex / regulation of mRNA stability / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / regulation of DNA-templated transcription elongation / transcription elongation factor complex / response to reactive oxygen species / cytosolic ribosome assembly / ribosome assembly / assembly of large subunit precursor of preribosome / transcription antitermination / DNA endonuclease activity / translational initiation / regulation of cell growth / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / large ribosomal subunit / ribosomal small subunit assembly / transferase activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / hydrolase activity / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 signature. ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / Ribosomal protein L9 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L21, conserved site / : / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L28/L24 superfamily / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / : / Ribosomal protein S19, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S4, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / : / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal protein S18, conserved site / Ribosomal L28 family / Ribosomal protein S18 signature. / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / Ribosomal protein L16 / Ribosomal protein S15, bacterial-type
Similarity search - Domain/homology
: / SPECTINOMYCIN / VALINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...: / SPECTINOMYCIN / VALINE / : / : / : / 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 / 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 / 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 (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsSteinmetzger, C. / Riad, M. / Petzold, K.
Funding supportEuropean Union, Sweden, 11items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 1011-2020European Union
H2020 Marie Curie Actions of the European Commission747446European Union
The Swedish Foundation for Strategic ResearchICA14-0023 Sweden
Swedish Research Council2014-04303 Sweden
Swedish Research Council2018-00250 Sweden
Ake Wiberg Foundation467080968European Union
Ake Wiberg FoundationM14-0109European Union
Other privateJS20140009 Sweden
Carl Trygger FoundationCTS14-383 Sweden
Carl Trygger FoundationCTS15-383 Sweden
Other privateM91/14 Sweden
CitationJournal: Biorxiv / Year: 2026
Title: Universal 3D Motif dynamics in RNA: The A-minor Switch
Authors: Steinmetzger, C. / Karlsson, H. / Fontana, C. / Galindo Riera, N. / Riad, M. / Kosek, D. / Schlagnitweit, J. / Steiner, E. / Friebe Sandoz, S. / Andersson, E.R. / Petzold, K.
History
DepositionFeb 20, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
3: Large ribosomal subunit protein bL36A
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
N: Small ribosomal subunit protein uS14
b: 5S rRNA
c: Large ribosomal subunit protein uL2
d: Large ribosomal subunit protein uL3
l: Large ribosomal subunit protein uL16
m: Large ribosomal subunit protein bL17
z: Large ribosomal subunit protein bL32
4: Large ribosomal subunit protein bL31
A: 16S rRNA
Y: A-site Val-tRNA^Val
Z: P-site tRNA^fMet
a: 23S rRNA
0: Large ribosomal subunit protein bL33
1: Large ribosomal subunit protein bL34
2: Large ribosomal subunit protein bL35
B: Small ribosomal subunit protein uS2
C: Small ribosomal subunit protein uS3
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6, fully modified isoform
G: Small ribosomal subunit protein uS7
H: Small ribosomal subunit protein uS8
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
M: Small ribosomal subunit protein uS13
O: Small ribosomal subunit protein uS15
P: Small ribosomal subunit protein bS16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18
S: Small ribosomal subunit protein uS19
T: Small ribosomal subunit protein bS20
U: Small ribosomal subunit protein bS21
X: mRNA
e: Large ribosomal subunit protein uL4
f: Large ribosomal subunit protein uL5
g: Large ribosomal subunit protein uL6
h: Large ribosomal subunit protein bL9
i: Large ribosomal subunit protein uL13
j: Large ribosomal subunit protein uL14
k: Large ribosomal subunit protein uL15
n: Large ribosomal subunit protein uL18
o: Large ribosomal subunit protein bL19
p: Large ribosomal subunit protein bL20
q: Large ribosomal subunit protein bL21
r: Large ribosomal subunit protein uL22
s: Large ribosomal subunit protein uL23
t: Large ribosomal subunit protein uL24
u: Large ribosomal subunit protein bL25
v: Large ribosomal subunit protein bL27
w: Large ribosomal subunit protein bL28
x: Large ribosomal subunit protein uL29
y: Large ribosomal subunit protein uL30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,202,466360
Polymers2,193,47555
Non-polymers8,991305
Water104,9375825
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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Large ribosomal subunit protein ... , 29 types, 29 molecules 3cdlmz4012efghijknopqrstuvwxy

#1: Protein/peptide Large ribosomal subunit protein bL36A / 50S ribosomal protein L36 / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7Q6
#6: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P60422
#7: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 22291.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P60438
#8: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15343.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0ADY7
#9: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0AG44
#10: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7N4
#11: Protein Large ribosomal subunit protein bL31 / 50S ribosomal protein L31


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7M9
#16: Protein Large ribosomal subunit protein bL33 / 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7N9
#17: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7P5
#18: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35 / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7Q1
#37: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P60723
#38: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P62399
#39: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0AG55
#40: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7R1
#41: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0AA10
#42: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0ADY3
#43: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P02413
#44: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0C018
#45: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7K6
#46: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7L3
#47: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0AG48
#48: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P61175
#49: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0ADZ0
#50: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P60624
#51: Protein Large ribosomal subunit protein bL25 / 50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P68919
#52: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7L8
#53: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7M2
#54: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7M6
#55: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0AG51

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Small ribosomal subunit protein ... , 20 types, 20 molecules KLNBCDEFGHIJMOPQRSTU

#2: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13871.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7R9
#3: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13814.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7S3
#4: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0AG59
#19: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7V0
#20: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7V3
#21: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7V8
#22: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7W1
#23: Protein Small ribosomal subunit protein bS6, fully modified isoform


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P02358
#24: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P02359
#25: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7W7
#26: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7X3
#27: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10 / Transcription termination/antitermination protein NusE


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7R5
#28: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7S9
#29: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0ADZ4
#30: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7T3
#31: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0AG63
#32: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7T7
#33: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7U3
#34: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P0A7U7
#35: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: UniProt: P68679

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RNA chain , 6 types, 6 molecules bAYZaX

#5: RNA chain 5S rRNA


Mass: 38790.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: SQ171fg / Plasmid: pAM552 / Production host: Escherichia coli (E. coli) / Strain (production host): SQ171fg / References: GenBank: CP035706.1
#12: RNA chain 16S rRNA


Mass: 499834.344 Da / Num. of mol.: 1 / Mutation: G1260U
Source method: isolated from a genetically manipulated source
Details: 16S rRNA with G1260U mutation affecting the conformational ground state of h41
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: SQ171fg / Plasmid: pAM552 / Production host: Escherichia coli (E. coli) / Strain (production host): SQ171fg / References: GenBank: 2971070070
#13: RNA chain A-site Val-tRNA^Val


Mass: 24542.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg / References: GenBank: 1845258627
#14: RNA chain P-site tRNA^fMet


Mass: 25229.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg
#15: RNA chain 23S rRNA


Mass: 941811.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: SQ171fg / Plasmid: pAM552 / Production host: Escherichia coli (E. coli) / Strain (production host): SQ171fg
#36: RNA chain mRNA


Mass: 3209.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: SQ171fg

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Non-polymers , 6 types, 6130 molecules

#56: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#57: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 227 / Source method: obtained synthetically / Formula: Mg
#58: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 74 / Source method: obtained synthetically / Formula: K
#59: Chemical ChemComp-SCM / SPECTINOMYCIN / ACTINOSPECTACIN / ESPECTINOMICINA / CHX-3101


Mass: 332.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H24N2O7 / Comment: antibiotic*YM
#60: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#61: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5825 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: E. coli 70S ribosome / Type: RIBOSOME / Entity ID: #1-#55 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: SQ171fg
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm / C2 aperture diameter: 20 µm
Image recordingElectron dose: 49.88 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.1particle selection
2EPUimage acquisition
4cryoSPARC4.5.1CTF correction
7UCSF ChimeraX1.8model fitting
9REFMAC5.8.0430model refinement
10cryoSPARC4.5.1initial Euler assignment
11cryoSPARC4.6.2final Euler assignment
12cryoSPARC4.5.1classification
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23232 / Symmetry type: POINT
Atomic model buildingSpace: RECIPROCAL
Atomic model buildingPDB-ID: 7K00

7k00


Accession code: 7K00 / Source name: PDB / Type: experimental model
RefinementResolution: 2.24→2.24 Å / Cor.coef. Fo:Fc: 0.785 / WRfactor Rwork: 0.327 / SU B: 7.43 / SU ML: 0.162 / Average fsc free: 0 / Average fsc overall: 0.7348 / Average fsc work: 0.7348 / ESU R: 0.146
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.327 3836702 -
all0.327 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 57.013 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0040.011156152
ELECTRON MICROSCOPYr_bond_other_d00.01790565
ELECTRON MICROSCOPYr_angle_refined_deg0.7441.845231298
ELECTRON MICROSCOPYr_angle_other_deg0.2781.732213617
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.47955645
ELECTRON MICROSCOPYr_dihedral_angle_2_deg3.2285576
ELECTRON MICROSCOPYr_dihedral_angle_other_2_deg0.47553636
ELECTRON MICROSCOPYr_dihedral_angle_3_deg10.033108684
ELECTRON MICROSCOPYr_dihedral_angle_6_deg10.007101965
ELECTRON MICROSCOPYr_chiral_restr0.0290.229531
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.02108936
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0228035
ELECTRON MICROSCOPYr_nbd_refined0.1420.221631
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1790.286641
ELECTRON MICROSCOPYr_nbtor_refined0.2210.257900
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0730.253465
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1150.29225
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0210.26
ELECTRON MICROSCOPYr_metal_ion_refined0.0690.21
ELECTRON MICROSCOPYr_mcbond_it1.6536.58522747
ELECTRON MICROSCOPYr_mcbond_other1.6536.58522747
ELECTRON MICROSCOPYr_mcangle_it3.00211.83128342
ELECTRON MICROSCOPYr_mcangle_other3.00211.83228343
ELECTRON MICROSCOPYr_scbond_it1.3975.588133405
ELECTRON MICROSCOPYr_scbond_other1.3975.588133382
ELECTRON MICROSCOPYr_scangle_it2.47110.203202956
ELECTRON MICROSCOPYr_scangle_other2.47110.203202957
ELECTRON MICROSCOPYr_lrange_it4.68162.174197417
ELECTRON MICROSCOPYr_lrange_other4.68162.174197418
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.08-2.1340.552843570.552843570.4310.55
2.134-2.1930.5062765980.5062765980.4870.506
2.193-2.2560.492692320.492692320.5360.49
2.256-2.3250.4752612910.4752612910.5760.475
2.325-2.4020.4562532400.4562532400.6220.456
2.402-2.4860.4372449600.4372449600.6620.437
2.486-2.580.4152362720.4152362720.7040.415
2.58-2.6850.3912276930.3912276930.7490.391
2.685-2.8050.3592180810.3592180810.7940.359
2.805-2.9410.3162084970.3162084970.8480.316
2.941-3.1010.2661981210.2661981210.9020.266
3.101-3.2890.2311877150.2311877150.9360.231
3.289-3.5160.2211762080.2211762080.9450.221
3.516-3.7970.221639180.221639180.9460.22
3.797-4.160.2141508150.2141508150.9460.214
4.16-4.650.2181364660.2181364660.9410.218
4.65-5.370.2251201720.2251201720.9330.225
5.37-6.5760.2481016950.2481016950.9160.248
6.576-9.2970.284784260.284784260.9060.284
9.297-277.2450.439429620.439429620.8650.439

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