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- PDB-9fbv: 70S Escherichia coli ribosome with P-site initiatior tRNA. -

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Basic information

Entry
Database: PDB / ID: 9fbv
Title70S Escherichia coli ribosome with P-site initiatior tRNA.
Components
  • (30S ribosomal protein ...) x 5
  • (50S ribosomal protein ...) x 2
  • (Large ribosomal subunit protein ...) x 27
  • (Small ribosomal subunit protein ...) x 15
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • fMet-tRNA
  • messenger RNA
KeywordsRIBOSOME / 70S / Initiation / fMet
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...negative regulation of cytoplasmic translational initiation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / translational initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / DNA endonuclease activity / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of 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
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 S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 ...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 S21 / 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 L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L17 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / 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 S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein L20 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein L27 signature. / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 ...: / : / : / 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 BW25113 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsKoller, T.O. / Wilson, D.N.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: bioRxiv / Year: 2024
Title: Paenilamicins from the honey bee pathogen are context-specific translocation inhibitors of protein synthesis.
Authors: Timm O Koller / Max J Berger / Martino Morici / Helge Paternoga / Timur Bulatov / Adriana Di Stasi / Tam Dang / Andi Mainz / Karoline Raulf / Caillan Crowe-McAuliffe / Marco Scocchi / Mario ...Authors: Timm O Koller / Max J Berger / Martino Morici / Helge Paternoga / Timur Bulatov / Adriana Di Stasi / Tam Dang / Andi Mainz / Karoline Raulf / Caillan Crowe-McAuliffe / Marco Scocchi / Mario Mardirossian / Bertrand Beckert / Nora Vázquez-Laslop / Alexander Mankin / Roderich D Süssmuth / Daniel N Wilson /
Abstract: The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen that display activity against Gram-positive pathogens, such as . While ...The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen that display activity against Gram-positive pathogens, such as . While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here, we have determined structures of the paenilamicin PamB2 stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site tRNAs. In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms utilized by . We could further demonstrate that PamB2 interferes with the translocation of mRNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a new class of context-specific translocation inhibitors.
History
DepositionMay 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: Large ribosomal subunit protein bL33
1: Large ribosomal subunit protein bL34
2: Large ribosomal subunit protein bL35
3: Large ribosomal subunit protein bL36A
b: 5S ribosomal RNA
c: Large ribosomal subunit protein uL2
d: Large ribosomal subunit protein uL3
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
k: 50S ribosomal protein L15
l: Large ribosomal subunit protein uL16
m: Large ribosomal subunit protein bL17
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: 50S ribosomal protein L25
v: Large ribosomal subunit protein bL27
w: Large ribosomal subunit protein bL28
x: Large ribosomal subunit protein uL29
y: Large ribosomal subunit protein uL30
z: Large ribosomal subunit protein bL32
4: Large ribosomal subunit protein bL31A
a: 23S ribosomal RNA
j: Large ribosomal subunit protein uL14
B: 30S ribosomal protein S2
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: 30S ribosomal protein S6, fully modified isoform
H: Small ribosomal subunit protein uS8
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
O: Small ribosomal subunit protein uS15
P: 30S ribosomal protein S16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18
T: 30S ribosomal protein S20
U: Small ribosomal subunit protein bS21
X: messenger RNA
C: Small ribosomal subunit protein uS3
G: 30S ribosomal protein S7
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14
S: Small ribosomal subunit protein uS19
A: 16S ribosomal RNA
Z: fMet-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,171,112365
Polymers2,163,42654
Non-polymers7,685311
Water70339
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 ... , 27 types, 27 molecules 0123cdefghilmnopqrstvwxyz4j

#1: 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 BW25113 (bacteria) / References: UniProt: P0A7N9
#2: 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 BW25113 (bacteria) / References: UniProt: P0A7P5
#3: 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 BW25113 (bacteria) / References: UniProt: P0A7Q1
#4: 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 BW25113 (bacteria) / 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 BW25113 (bacteria) / 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 BW25113 (bacteria) / References: UniProt: P60438
#8: 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 BW25113 (bacteria) / References: UniProt: P60723
#9: 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 BW25113 (bacteria) / References: UniProt: P62399
#10: 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 BW25113 (bacteria) / References: UniProt: P0AG55
#11: 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 BW25113 (bacteria) / References: UniProt: P0A7R1
#12: 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 BW25113 (bacteria) / References: UniProt: P0AA10
#14: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15329.343 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0ADY7
#15: 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 BW25113 (bacteria) / References: UniProt: P0AG44
#16: 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 BW25113 (bacteria) / References: UniProt: P0C018
#17: 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 BW25113 (bacteria) / References: UniProt: P0A7K6
#18: 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 BW25113 (bacteria) / References: UniProt: P0A7L3
#19: 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 BW25113 (bacteria) / References: UniProt: P0AG48
#20: 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 BW25113 (bacteria) / References: UniProt: P61175
#21: 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 BW25113 (bacteria) / References: UniProt: P0ADZ0
#22: 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 BW25113 (bacteria) / References: UniProt: P60624
#24: 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 BW25113 (bacteria) / References: UniProt: P0A7L8
#25: 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 BW25113 (bacteria) / References: UniProt: P0A7M2
#26: 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 BW25113 (bacteria) / References: UniProt: P0A7M6
#27: 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 BW25113 (bacteria) / References: UniProt: P0AG51
#28: 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 BW25113 (bacteria) / References: UniProt: P0A7N4
#29: Protein Large ribosomal subunit protein bL31A / 50S ribosomal protein L31


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7M9
#31: 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 BW25113 (bacteria) / References: UniProt: P0ADY3

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RNA chain , 5 types, 5 molecules baXAZ

#5: RNA chain 5S ribosomal RNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1845258627
#30: RNA chain 23S ribosomal RNA


Mass: 941505.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)
#45: RNA chain messenger RNA


Mass: 935.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria)
#53: RNA chain 16S ribosomal RNA


Mass: 497348.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1789840096
#54: RNA chain fMet-tRNA


Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1845258627

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50S ribosomal protein ... , 2 types, 2 molecules ku

#13: Protein 50S ribosomal protein L15 / Large ribosomal subunit protein uL15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02413
#23: Protein 50S ribosomal protein L25 / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P68919

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30S ribosomal protein ... , 5 types, 5 molecules BFPTG

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


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V0
#35: Protein 30S ribosomal protein S6, fully modified isoform


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02358
#40: Protein 30S ribosomal protein S16 / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7T3
#43: Protein 30S ribosomal protein S20 / Small ribosomal subunit protein bS20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7U7
#47: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02359

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Small ribosomal subunit protein ... , 15 types, 15 molecules DEHKLOQRUCIJMNS

#33: 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 BW25113 (bacteria) / References: UniProt: P0A7V8
#34: 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 BW25113 (bacteria) / References: UniProt: P0A7W1
#36: 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 BW25113 (bacteria) / References: UniProt: P0A7W7
#37: 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 BW25113 (bacteria) / References: UniProt: P0A7R9
#38: 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 BW25113 (bacteria) / References: UniProt: P0A7S3
#39: 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 BW25113 (bacteria) / References: UniProt: P0ADZ4
#41: 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 BW25113 (bacteria) / References: UniProt: P0AG63
#42: 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 BW25113 (bacteria) / References: UniProt: P0A7T7
#44: 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 BW25113 (bacteria) / References: UniProt: P68679
#46: 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 BW25113 (bacteria) / References: UniProt: P0A7V3
#48: 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 BW25113 (bacteria) / References: UniProt: P0A7X3
#49: 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 BW25113 (bacteria) / References: UniProt: P0A7R5
#50: 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 BW25113 (bacteria) / References: UniProt: P0A7S9
#51: 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 BW25113 (bacteria) / References: UniProt: P0AG59
#52: 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 BW25113 (bacteria) / References: UniProt: P0A7U3

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Non-polymers , 4 types, 350 molecules

#55: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 306 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#58: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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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: Escherichia coli 70S Initiation complex with P-site initiator tRNA fMet
Type: RIBOSOME
Details: Escherichia coli 70S Initiation complex with P-site initiator tRNA fMet
Entity ID: #1-#35, #37-#54 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 8 OD/mL of Ribosome
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 900 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: REFMAC / Version: 5.8.0425 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84771 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7K00

7k00


Accession code: 7K00 / Details: Ribosome (ribosomal proteins and ribosomal RNA) / Source name: PDB / Type: experimental model
RefinementResolution: 2.4→281.6 Å / Cor.coef. Fo:Fc: 0.747 / SU B: 8.634 / SU ML: 0.179 / ESU R: 0.207
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.33376 --
obs0.33376 2654949 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 57.805 Å2
Refinement stepCycle: 1 / Total: 140097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.011152165
ELECTRON MICROSCOPYr_bond_other_d0.0010.01788924
ELECTRON MICROSCOPYr_angle_refined_deg1.0371.846227134
ELECTRON MICROSCOPYr_angle_other_deg0.4191.732209744
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.80355530
ELECTRON MICROSCOPYr_dihedral_angle_2_deg3.0232.097558
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.568108534
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0460.228986
ELECTRON MICROSCOPYr_gen_planes_refined0.010.02106893
ELECTRON MICROSCOPYr_gen_planes_other0.0030.0227546
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it4.7596.01822291
ELECTRON MICROSCOPYr_mcbond_other4.7596.01822291
ELECTRON MICROSCOPYr_mcangle_it7.80310.83227768
ELECTRON MICROSCOPYr_mcangle_other7.80310.83327769
ELECTRON MICROSCOPYr_scbond_it4.6275.698129874
ELECTRON MICROSCOPYr_scbond_other4.6275.698129874
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other7.68410.324199367
ELECTRON MICROSCOPYr_long_range_B_refined11.73761.83194697
ELECTRON MICROSCOPYr_long_range_B_other11.73761.83194696
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.702 196415 -
obs--100 %

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