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- PDB-8t5d: Cryo-EM studies of the interplay between uS2 ribosomal protein an... -

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Basic information

Entry
Database: PDB / ID: 8t5d
TitleCryo-EM studies of the interplay between uS2 ribosomal protein and leaderless mRNA during bacterial translation initiation
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 26
  • 16s RNA
  • 23S RNA
  • 5S RNA
  • Ribosomal protein L21
  • Transcription termination/antitermination protein NusG
  • lmRNA
  • tRNA
KeywordsRIBOSOME / leaderless mRNA / Cryo-EM / 70S / HflX / bS21 / uS2
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding ...transcription elongation-coupled chromatin remodeling / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / Ribosomal protein S21, conserved site ...: / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / 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 L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / 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 L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L34, conserved site / Ribosomal L28 family / Ribosomal protein L34 signature. / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein L20 / Ribosomal protein S15, bacterial-type / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein S6 / Ribosomal protein L19
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS17 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL17 / Transcription termination/antitermination protein NusG / 30S ribosomal protein S21 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Bacteriophage sp. (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBhattacharjee, S. / Gottesman, M.E. / Frank, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM139453 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA174653 United States
CitationJournal: J Mol Biol / Year: 2024
Title: How Dedicated Ribosomes Translate a Leaderless mRNA.
Authors: Francisco J Acosta-Reyes / Sayan Bhattacharjee / Max Gottesman / Joachim Frank /
Abstract: In bacteriophage λ lysogens, the λcI repressor is encoded by the leaderless transcript (lmRNA) initiated at the λpRM promoter. Translation is enhanced in rpsB mutants deficient in ribosomal ...In bacteriophage λ lysogens, the λcI repressor is encoded by the leaderless transcript (lmRNA) initiated at the λpRM promoter. Translation is enhanced in rpsB mutants deficient in ribosomal protein uS2. Although translation initiation of lmRNA is conserved in bacteria, archaea, and eukaryotes, structural insight of a lmRNA translation initiation complex is missing. Here, we use cryo-EM to solve the structures of the uS2-deficient 70S ribosome of host E. coli mutant rpsB11 and the wild-type 70S complex with λcI lmRNA and fMet-tRNA. Importantly, the uS2-deficient 70S ribosome also lacks protein bS21. The anti-Shine-Dalgarno (aSD) region is structurally supported by bS21, so that the absence of the latter causes the aSD to divert from the normal mRNA exit pathway, easing the exit of lmRNA. A π-stacking interaction between the monitor base A1493 and A(+4) of lmRNA potentially acts as a recognition signal. Coulomb charge flow, along with peristalsis-like dynamics within the mRNA entrance channel due to the increased 30S head rotation caused by the absence of uS2, are likely to facilitate the propagation of lmRNA through the ribosome. These findings lay the groundwork for future research on the mechanism of translation and the co-evolution of lmRNA and mRNA that includes the emergence of a defined ribosome-binding site of the transcript.
History
DepositionJun 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
A: 5S RNA
B: 23S 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
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: 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: 30S ribosomal protein S2
b: 30S ribosomal protein S3
c: 30S ribosomal protein S4
d: 30S ribosomal protein S5
e: 30S ribosomal protein S6, non-modified isoform
f: 30S ribosomal protein S7
g: 30S ribosomal protein S8
h: 30S ribosomal protein S9
i: 30S ribosomal protein S10
j: 30S ribosomal protein S11
k: 30S ribosomal protein S12
l: 30S ribosomal protein S13
m: 30S ribosomal protein S14
n: 30S ribosomal protein S15
o: 30S ribosomal protein S16
p: 30S ribosomal protein S17
q: 30S ribosomal protein S18
r: 30S ribosomal protein S19
s: 30S ribosomal protein S20
t: 30S ribosomal protein S21 (Fragment)
u: Transcription termination/antitermination protein NusG
v: 16s RNA
x: lmRNA
5: tRNA


Theoretical massNumber of molelcules
Total (without water)2,120,50753
Polymers2,120,50753
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 26 types, 26 molecules 01234CDEFGJKLMNOPQSTUVWXYZ

#1: Protein 50S ribosomal protein L32


Mass: 6332.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmF, ECDEC2D_1303 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A828UBL8
#2: Protein 50S ribosomal protein L33


Mass: 5928.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmG, CSW52_15065 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A891SPC3
#3: Protein/peptide 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmH / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGC4
#4: Protein 50S ribosomal protein L35


Mass: 7181.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmI, ERFG_01622 / Production host: Escherichia coli (E. coli) / References: UniProt: E9XJC8
#5: Protein/peptide 50S ribosomal protein L36


Mass: 4377.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmJ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2L017
#8: Protein 50S ribosomal protein L2


Mass: 29792.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplB, ECVG_03081 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3JB59
#9: Protein 50S ribosomal protein L3 / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplC, b3320, JW3282 / Production host: Escherichia coli (E. coli) / References: UniProt: P60438
#10: Protein 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: A1AGK6
#11: Protein 50S ribosomal protein L5


Mass: 20202.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplE / Production host: Escherichia coli (E. coli) / References: UniProt: D6IEK6
#12: Protein 50S ribosomal protein L6


Mass: 18801.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: G736_03813 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8E0IYC4
#13: Protein 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplM, A1UI_03510 / Production host: Escherichia coli (E. coli) / References: UniProt: S1EW51
#14: Protein 50S ribosomal protein L14


Mass: 13433.872 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplN / Production host: Escherichia coli (E. coli) / References: UniProt: C3SQZ2
#15: Protein 50S ribosomal protein L15


Mass: 14877.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: rplO, A8C65_19395, A9R57_24660, ACU57_21045, AM464_09135, AUQ13_22145, BHS87_18545, BJJ90_02210, BUE81_25610, BW690_10710, BZL31_22885, C5N07_23575, C9E25_20065, CA593_09735, CG692_20270, D0X26_ ...Gene: rplO, A8C65_19395, A9R57_24660, ACU57_21045, AM464_09135, AUQ13_22145, BHS87_18545, BJJ90_02210, BUE81_25610, BW690_10710, BZL31_22885, C5N07_23575, C9E25_20065, CA593_09735, CG692_20270, D0X26_24495, DNQ41_22370, DTL43_21000, EC1094V2_354, EC3234A_55c00230, EL75_0396, EL79_0415, EL80_0407, ERS085365_03907, ERS085416_03881, ERS139211_03685, ERS150873_04051, NCTC11022_03475, NCTC11126_02772, NCTC13462_04101, NCTC9010_00498, NCTC9037_00664, NCTC9045_00567, NCTC9062_02686, NCTC9117_00757, NCTC9706_02738, RK56_021420, SAMEA3472047_03862, SAMEA3472067_03530, SAMEA3472080_04748, SAMEA3484427_04887, SAMEA3484429_04875, SAMEA3484433_04924, SAMEA3752559_00346, SAMEA3753106_04635, SAMEA3753300_02227, SAMEA3753391_02957, SAMEA3753397_02423
Production host: Escherichia coli (E. coli) / References: UniProt: A0A037Y8L6
#16: Protein 50S ribosomal protein L16 / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplP, b3313, JW3275 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY7
#17: Protein 50S ribosomal protein L17


Mass: 13851.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: rplQ, E3N34_07125, H0O51_24700, NCTC10767_01524, NCTC9081_00927
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2T1LEK9
#18: Protein 50S ribosomal protein L18


Mass: 12663.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplR, EAVG_03042 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3KXD9
#19: Protein 50S ribosomal protein L19


Mass: 13028.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplS, A13A_02795 / Production host: Escherichia coli (E. coli) / References: UniProt: S1PSA3
#20: Protein 50S ribosomal protein L20


Mass: 13396.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplT, A311_02335 / Production host: Escherichia coli (E. coli) / References: UniProt: L4J8J1
#22: Protein 50S ribosomal protein L22 / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplV, eryB, b3315, JW3277 / Production host: Escherichia coli (E. coli) / References: UniProt: P61175
#23: Protein 50S ribosomal protein L23


Mass: 10661.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplW, A1UI_03591 / Production host: Escherichia coli (E. coli) / References: UniProt: S1EUY1
#24: Protein 50S ribosomal protein L24


Mass: 11208.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplX / Production host: Escherichia coli (E. coli) / References: UniProt: S1E9P3
#25: Protein 50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplY / Production host: Escherichia coli (E. coli) / References: UniProt: D7XH79
#26: Protein 50S ribosomal protein L27


Mass: 8476.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmA / Production host: Escherichia coli (E. coli) / References: UniProt: C3SSG7
#27: Protein 50S ribosomal protein L28


Mass: 8896.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmB, G925_03874 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2KZD0
#28: Protein 50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmC, ECDG_03892 / Production host: Escherichia coli (E. coli) / References: UniProt: D6IEL0
#29: Protein 50S ribosomal protein L30 / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmD, b3302, JW3264 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG51

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RNA chain , 5 types, 5 molecules ABvx5

#6: RNA chain 5S RNA


Mass: 37848.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1845258627
#7: RNA chain 23S RNA


Mass: 941306.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 937521852
#51: RNA chain 16s RNA


Mass: 498725.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1338015391
#52: RNA chain lmRNA


Mass: 3866.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage sp. (virus) / Production host: Bacteriophage sp. (virus)
#53: RNA chain tRNA


Mass: 24802.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1848934315

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Protein , 2 types, 2 molecules Ru

#21: Protein Ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplU, ECMP0215528_3699 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A829CSJ4
#50: Protein Transcription termination/antitermination protein NusG


Mass: 6639.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nusG / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2X1MT45

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

#30: Protein 30S ribosomal protein S2


Mass: 24253.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsB, HMPREF1620_04659 / Production host: Escherichia coli (E. coli) / References: UniProt: U9ZNW8
#31: Protein 30S ribosomal protein S3


Mass: 23078.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsC / Production host: Escherichia coli (E. coli) / References: UniProt: V0Y888
#32: Protein 30S ribosomal protein S4


Mass: 23383.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: rpsD, rpsD_2, A2F99_003133, A5U30_004530, A6592_25685, A8499_003310, A8502_004045, A8X14_004364, A9X72_02295, AAG43_004468, AAG80_001471, AAG81_002934, AAS29_002184, ACN68_01785, ACN81_25410, ...Gene: rpsD, rpsD_2, A2F99_003133, A5U30_004530, A6592_25685, A8499_003310, A8502_004045, A8X14_004364, A9X72_02295, AAG43_004468, AAG80_001471, AAG81_002934, AAS29_002184, ACN68_01785, ACN81_25410, ACU57_21070, AM464_09110, APX88_16185, AT845_004400, AW118_24790, AW119_26600, AWP47_12755, B6R12_002829, B6R15_004091, B6R31_004990, B6R48_005057, B6R87_004967, BANRA_04306, BANRA_04454, BEA19_23315, BER14_25080, BF481_004952, BG944_001111, BGM66_003615, BHS81_19725, BJI68_08785, BJJ90_02235, BK292_20395, BK383_24755, BKL28_004565, BLM69_000018, BMC79_004441, BMO21_000808, BMT50_12325, BMT91_19960, BO178_004290, BON92_01160, BR158_003768, BRV02_004619, BRV34_003992, BRV41_004380, BSR05_22680, BTB68_004378, BTQ06_10580, BUO55_004719, BvCmsHHP019_04126, BvCmsHHP056_02698, BvCmsKKP061_03008, BvCmsKSNP073_02050, BXT93_05585, BZL69_25920, C0P57_002646, C1Q91_004926, C2121_004184, C2M16_25515, C2R31_004611, C3F40_19830, C5N07_23600, C9114_23780, C9E67_02835, C9Z68_22525, CA593_09760, CCS08_00105, CCV24_003537, CDL36_25620, CDL37_18565, CF22_004871, CG831_003627, CIG67_10785, CO706_15175, CQ986_004903, CQB02_00600, CR538_02530, CR539_21790, CR628_001344, CSE52_004356, CTR35_003608, CWS33_24830, CX690_001674, CX691_001950, CX692_003176, CX693_003183, CX694_003140, CX696_002237, CX699_003071, CX938_003809, CY655_21210, CYM75_002789, D0X26_24470, D1912_27635, D3C88_00295, D3G36_23160, D4M65_20545, D4N09_20145, D4U49_16120, D9D43_22660, D9E34_23635, D9E49_05130, D9H94_20860, D9J03_20025, D9J61_16625, DD762_23520, DIV22_15285, DN627_24395, DNQ45_03730, DNX30_25505, DRW19_25110, DS732_24235, DTL43_21025, DTL90_24665, DTM45_24580, DU321_11975, E0I42_22165, E3N34_07135, E4K51_21465, E5H86_24550, E6D34_21785, EA239_22765, EA435_23005, EAI46_07450, EAX79_10685, EBP16_21900, EC95NR1_02686, ECs4161, EHD79_24265, EIA08_23930, EIZ93_12495, EKI52_17690, EL79_0420, ELT17_22465, ELT48_22895, ELV28_22900, ELX68_21515, ELX69_22945, ELX76_22915, ELX79_22025, ELX96_16780, ELY32_12890, ELY41_18695, ELY48_23135, EN85_004371, EPS76_07240, ERS085406_04412, ERS085411_04292, ERS139208_04360, EWK56_24970, ExPECSC038_03662, F0L67_25290, F3N40_22390, F7F11_22750, F7N46_24035, F9413_21260, F9461_25680, F9B07_24710, F9S83_18965, F9U58_14355, F9V22_13840, FA868_22720, FDM60_20865, FEJ01_22540, FFF58_25480, FGG80_25160, FHD44_21240, FIJ20_21220, FJQ40_18280, FJQ53_22940, FKO60_25610, FNA08_03300, FOI11_019285, FOI11_03895, FPI65_20280, FPS11_25455, FTV90_00725, FTV93_20925, FV293_22490, FVB16_04845, FWK02_29585, FZN31_02660, FZU14_21795, G3565_26290, G3V95_19820, G3W53_20930, G4A38_21485, G4A47_20755, G5603_24560, G9448_17100, GAI89_24855, GAJ12_24745, GAJ26_21985, GF699_19710, GFY34_22925, GGB84_004473, GIB53_19425, GJ11_21360, GJO56_22710, GKF66_21520, GKF89_18445, GNW61_16605, GNZ05_26010, GOP25_22680, GP711_23280, GP944_18765, GP954_00970, GP965_04270, GP975_01160, GP979_02030, GQA06_03975, GQM04_10540, GQM13_25175, GQM21_11205, GQN34_23240, GQW07_21575, GRC73_21775, GRO95_20840, GRW05_09035, GRW24_04780, GRW56_00270, GRW57_03565, GSM54_23355, GSY44_19975, GUC01_21155, GUI33_20020, H0O51_24710, H0O53_20855, H0O72_19390, H6Y26_003158, HCQ42_003954, HEP30_018610, HEP34_004776, HHH44_004541, HI055_004134, HIE29_005181, HJ942_004444, HJQ60_005017, HKA49_005041, HL563_21575, HL601_22380, HLV18_23365, HLX92_10100, HLZ50_22205, HMV95_19580, HMW38_23080, HV109_02215, HV146_21645, HV209_14740, HVV39_09240, HVW04_17560, HVW43_18695, HVX31_01995, HVX32_19020, HVY77_02200, HVZ29_19070, HVZ30_02080, HVZ71_02385, HX136_02220, I6H00_20950, I6H02_11965, IA00_004082, IFB95_004800, IH772_24040, IT029_004959, J0541_004391, J4S20_004808, J5U05_004093, JFD_03707, JNP96_25280, NCTC10082_02845, NCTC10089_00508, NCTC10090_03533, NCTC10418_00697, NCTC10429_01101, NCTC10764_03869, NCTC10767_01522, NCTC10865_00667, NCTC10974_00558, NCTC11112_01030, NCTC11126_02778, NCTC11181_02744, NCTC11341_01883, NCTC12950_00485, NCTC13127_00793, NCTC13148_03435, NCTC13216_01346, NCTC4450_02481, NCTC7922_04037, NCTC7927_00557, NCTC7928_02509, NCTC8009_01519, NCTC8179_05949, NCTC8333_00495, NCTC8450_04944, NCTC8621_00514, NCTC8622_00500, NCTC8959_03255, NCTC8960_03076, NCTC9001_04260, NCTC9044_01350, NCTC9045_00572, NCTC9075_00730, NCTC9077_00610, NCTC9081_00925, NCTC9111_00873, NCTC9117_00761, NCTC9702_00543, NCTC9706_02743, NCTC9775_04009, NCTC9777_01897, NCTC9962_06803, ND22_005162, RG28_21585, SAMEA3472044_01168, SAMEA3472056_05405, SAMEA3472147_04298, SAMEA3751407_00018, SAMEA3752557_01946, SAMEA3753106_04640, TUM18780_04410, WR15_19580
Production host: Escherichia coli (E. coli) / References: UniProt: C3SR62
#33: Protein 30S ribosomal protein S5


Mass: 15804.282 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsE, ECJG_02962 / Production host: Escherichia coli (E. coli) / References: UniProt: F4TL26
#34: Protein 30S ribosomal protein S6, non-modified isoform


Mass: 11669.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsF, b4200, JW4158 / Production host: Escherichia coli (E. coli) / References: UniProt: P02358
#35: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 16861.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsG, b3341, JW3303 / Production host: Escherichia coli (E. coli) / References: UniProt: P02359
#36: Protein 30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsH, ECDEC2D_3910 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A828U358
#37: Protein 30S ribosomal protein S9


Mass: 14554.882 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsI, HMPREF1599_00992 / Production host: Escherichia coli (E. coli) / References: UniProt: V0A2W7
#38: Protein 30S ribosomal protein S10


Mass: 11196.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsJ, NRG857_16455 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3EQD3
#39: Protein 30S ribosomal protein S11 / Small ribosomal subunit protein uS11


Mass: 12487.200 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsK, b3297, JW3259 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R9
#40: Protein 30S ribosomal protein S12


Mass: 13636.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsL, EC40522_4581 / Production host: Escherichia coli (E. coli) / References: UniProt: I2UHF1
#41: Protein 30S ribosomal protein S13


Mass: 12625.753 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsM, A13A_03621 / Production host: Escherichia coli (E. coli) / References: UniProt: S1P5F8
#42: Protein 30S ribosomal protein S14


Mass: 11489.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsN, ECIAI1_3456 / Production host: Escherichia coli (E. coli) / References: UniProt: B7M1M1
#43: Protein 30S ribosomal protein S15


Mass: 10159.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsO, HMPREF9536_02433 / Production host: Escherichia coli (E. coli) / References: UniProt: D7XN21
#44: Protein 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsP / Production host: Escherichia coli (E. coli) / References: UniProt: C3SYP2
#45: Protein 30S ribosomal protein S17


Mass: 9263.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsQ, AC28_3826 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A080IK26
#46: Protein 30S ribosomal protein S18


Mass: 6466.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsR / Production host: Escherichia coli (E. coli) / References: UniProt: W1EY92
#47: Protein 30S ribosomal protein S19


Mass: 9057.626 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsS, ECKIH15140_04691 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9LGZ0
#48: Protein 30S ribosomal protein S20


Mass: 9506.190 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsT / Production host: Escherichia coli (E. coli) / References: UniProt: C3TRH7
#49: Protein 30S ribosomal protein S21 (Fragment)


Mass: 6067.081 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsU / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C9AJ78

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Apo 70S at 900 ms / Type: RIBOSOME / Details: control experiment / Entity ID: #1-#51 / Source: NATURAL
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: DARK FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
4RELION4CTF correction
Image processingDetails: High-pass filtered
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004155304
ELECTRON MICROSCOPYf_angle_d0.815232725
ELECTRON MICROSCOPYf_dihedral_angle_d15.5461882
ELECTRON MICROSCOPYf_chiral_restr0.04329772
ELECTRON MICROSCOPYf_plane_restr0.00712217

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