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- PDB-9wnq: Structure of E.coli ribosome in complex with an engineered arrest... -

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Basic information

Entry
Database: PDB / ID: 9wnq
TitleStructure of E.coli ribosome in complex with an engineered arrest peptide
Components
  • (30S ribosomal protein ...) x 18
  • (50S ribosomal protein ...) x 13
  • (Large ribosomal subunit protein ...) x 15
  • (Small ribosomal subunit protein ...) x 2
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S rRNA
  • A-tRNA(PRO),P-tRNA(PRO)
  • E-site tRNA
  • eRAP-NC
  • mRNA
KeywordsRIBOSOME / Ribosomal nascent chain / ribosomal arrest peptide / ribosomal translation / ribosome stalling
Function / homology
Function and homology information


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 ...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 / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / regulation of mRNA stability / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / ribosome assembly / regulation of DNA-templated transcription elongation / transcription elongation factor complex / cytosolic ribosome assembly / response to reactive oxygen species / DNA endonuclease activity / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosome biogenesis / large ribosomal subunit / regulation of translation / ribosome binding / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / 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 / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
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 L16 signature 1. ...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 L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein S6 superfamily
Similarity search - Domain/homology
PROLINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 ...PROLINE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / 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 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 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: 2.59 Å
AuthorsSriramoju, M.K. / Ko, T.P. / Draczkowski, P. / Hsu, S.T.D.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-CDA-109-L08, AS-CFII-111-210 Taiwan
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-001-050-MY3 and 110-2311-B-001-013-MY3, 110-2811-M-001-584, 111-2811-M-001-125, 112-2811-M-001-087 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural basis of enhanced stalling efficiency of an engineered ribosome arrest peptide
Authors: Sriramoju, M.K. / Ko, T.P. / Draczkowski, P. / Hsu, S.T.D.
History
DepositionSep 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: 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 bL28
1: Large ribosomal subunit protein uL29
2: Large ribosomal subunit protein uL30
4: Large ribosomal subunit protein bL32
5: Large ribosomal subunit protein bL33
6: 50S ribosomal protein L34
7: Large ribosomal subunit protein bL35
8: 50S ribosomal protein L36
A: 16S ribosomal RNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6, fully modified isoform
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein S21
X: E-site tRNA
Y: A-tRNA(PRO),P-tRNA(PRO)
Z: A-tRNA(PRO),P-tRNA(PRO)
a: 5S rRNA
b: 23S ribosomal RNA
c: Large ribosomal subunit protein uL2
d: 50S ribosomal protein L3
e: 50S ribosomal protein L4
f: Large ribosomal subunit protein uL5
g: Large ribosomal subunit protein uL6
h: 50S ribosomal protein L9
k: 50S ribosomal protein L13
l: 50S ribosomal protein L14
m: 50S ribosomal protein L15
n: 50S ribosomal protein L16
o: Large ribosomal subunit protein bL17
p: Large ribosomal subunit protein uL18
q: Large ribosomal subunit protein bL19
r: Large ribosomal subunit protein bL20
s: 50S ribosomal protein L21
t: 50S ribosomal protein L22
u: Large ribosomal subunit protein uL23
v: 50S ribosomal protein L24
w: 50S ribosomal protein L25
x: mRNA
y: Large ribosomal subunit protein bL27
z: eRAP-NC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,211,36958
Polymers2,211,18856
Non-polymers1812
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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Large ribosomal subunit protein ... , 15 types, 15 molecules 012457cfgopqruy

#1: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmB, b3637, JW3612 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7M2
#2: Protein Large ribosomal subunit protein uL29 / 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, b3312, JW3274 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7M6
#3: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6554.820 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
#4: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmF, b1089, JW1075 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7N4
#5: Protein Large ribosomal subunit protein bL33 / 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmG, b3636, JW3611 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7N9
#7: 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 genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmI, b1717, JW1707 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#34: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplB, b3317, JW3279 / Production host: Escherichia coli (E. coli) / References: UniProt: P60422
#37: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplE, b3308, JW3270 / Production host: Escherichia coli (E. coli) / References: UniProt: P62399
#38: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplF, b3305, JW3267 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG55
#44: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplQ, b3294, JW3256 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG44
#45: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplR, b3304, JW3266 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C018
#46: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13159.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplS, b2606, JW2587 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7K6
#47: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplT, pdzA, b1716, JW1706 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L3
#50: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplW, b3318, JW3280 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#54: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 9146.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmA, b3185, JW3152 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L8

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50S ribosomal protein ... , 13 types, 13 molecules 68dehklmnstvw

#6: Protein/peptide 50S ribosomal protein L34 / Large ribosomal subunit protein bL34


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, rimA, ssaF, b3703, JW3680 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7P5
#8: Protein/peptide 50S ribosomal protein L36 / Large ribosomal subunit protein bL36-A / Ribosomal protein B


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, b3299, JW3261 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Q6
#35: Protein 50S ribosomal protein L3


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 / Production host: Escherichia coli (E. coli) / References: UniProt: C3SQU2
#36: Protein 50S ribosomal protein L4 / Large ribosomal subunit protein uL4


Mass: 22121.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplD, eryA, b3319, JW3281 / Production host: Escherichia coli (E. coli) / References: UniProt: P60723
#39: Protein 50S ribosomal protein L9 / Large ribosomal subunit protein bL9


Mass: 15789.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplI, b4203, JW4161 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R1
#40: Protein 50S ribosomal protein L13 / Large ribosomal subunit protein uL13


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, b3231, JW3200 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA10
#41: Protein 50S ribosomal protein L14 / Large ribosomal subunit protein uL14


Mass: 13565.067 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplN, b3310, JW3272 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY3
#42: Protein 50S ribosomal protein L15 / Large ribosomal subunit protein uL15


Mass: 15008.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplO, b3301, JW3263 / Production host: Escherichia coli (E. coli) / References: UniProt: P02413
#43: 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
#48: Protein 50S ribosomal protein L21 / Large ribosomal subunit protein bL21


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, b3186, JW3153 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG48
#49: 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
#51: Protein 50S ribosomal protein L24 / Large ribosomal subunit protein uL24


Mass: 11339.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplX, b3309, JW3271 / Production host: Escherichia coli (E. coli) / References: UniProt: P60624
#52: Protein 50S ribosomal protein L25 / Large ribosomal subunit protein bL25


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, b2185, JW2173 / Production host: Escherichia coli (E. coli) / References: UniProt: P68919

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RNA chain , 6 types, 7 molecules AXYZabx

#9: RNA chain 16S ribosomal RNA


Mass: 496892.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 16S ribosomal RNA / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1388194076
#30: RNA chain E-site tRNA


Mass: 24478.502 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: 1609454293
#31: RNA chain A-tRNA(PRO),P-tRNA(PRO)


Mass: 24846.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#32: 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) / Production host: Escherichia coli (E. coli) / References: GenBank: 1370526514
#33: RNA chain 23S ribosomal RNA


Mass: 941612.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 23S ribosomal RNA / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 2096335303
#53: RNA chain mRNA


Mass: 4476.740 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)

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30S ribosomal protein ... , 18 types, 18 molecules BCDEFGHIJMNOPQRSTU

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


Mass: 26781.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsB, b0169, JW0164 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V0
#11: Protein 30S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 26031.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsC, b3314, JW3276 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V3
#12: Protein 30S ribosomal protein S4 / Small ribosomal subunit protein uS4


Mass: 23514.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsD, ramA, b3296, JW3258 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V8
#13: Protein 30S ribosomal protein S5 / Small ribosomal subunit protein uS5


Mass: 17629.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsE, spc, b3303, JW3265 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7W1
#14: Protein 30S ribosomal protein S6, fully modified isoform


Mass: 15727.512 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
#15: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 20055.156 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
#16: Protein 30S ribosomal protein S8 / Small ribosomal subunit protein uS8


Mass: 14146.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsH, b3306, JW3268 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7W7
#17: Protein 30S ribosomal protein S9 / Small ribosomal subunit protein uS9


Mass: 14886.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsI, b3230, JW3199 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7X3
#18: Protein 30S ribosomal protein S10 / Small ribosomal subunit protein uS10 / Transcription termination/antitermination protein NusE


Mass: 11755.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsJ, nusE, b3321, JW3283 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R5
#21: Protein 30S ribosomal protein S13 / Small ribosomal subunit protein uS13


Mass: 13128.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsM, b3298, JW3260 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7S9
#22: Protein 30S ribosomal protein S14 / Small ribosomal subunit protein uS14


Mass: 11606.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsN, b3307, JW3269 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG59
#23: Protein 30S ribosomal protein S15 / Small ribosomal subunit protein uS15


Mass: 10290.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsO, secC, b3165, JW3134 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#24: Protein 30S ribosomal protein S16 / Small ribosomal subunit protein bS16


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, b2609, JW2590 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7T3
#25: Protein 30S ribosomal protein S17 / Small ribosomal subunit protein uS17


Mass: 9724.491 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsQ, neaA, b3311, JW3273 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG63
#26: Protein 30S ribosomal protein S18 / Small ribosomal subunit protein bS18


Mass: 9005.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsR, b4202, JW4160 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7T7
#27: Protein 30S ribosomal protein S19 / Small ribosomal subunit protein uS19


Mass: 10455.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsS, b3316, JW3278 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7U3
#28: Protein 30S ribosomal protein S20 / Small ribosomal subunit protein bS20


Mass: 9708.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsT, b0023, JW0022 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7U7
#29: Protein 30S ribosomal protein S21 / Small ribosomal subunit protein bS21


Mass: 8524.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsU, b3065, JW3037 / Production host: Escherichia coli (E. coli) / References: UniProt: P68679

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Small ribosomal subunit protein ... , 2 types, 2 molecules KL

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


Mass: 13870.975 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
#20: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13768.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsL, strA, b3342, JW3304 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7S3

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Protein/peptide , 1 types, 1 molecules z

#55: Protein/peptide eRAP-NC


Mass: 3166.636 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: eRAP / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 2 molecules

#56: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#57: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2

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Details

Has ligand of interestN
Has protein modificationN

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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 in complex with eRAP / Type: RIBOSOME / Entity ID: #1-#55 / Source: RECOMBINANT
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
Details: 20 mM HEPES (pH 7.6), 140 mM NH4Cl, 25 mM MgCl2, 2 mM DTT
SpecimenConc.: 0.42 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: NITROGEN / Humidity: 100 % / Chamber temperature: 277.15 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 defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 38 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 2668

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7UCSF ChimeraX1.9model fitting
9cryoSPARC3.1initial Euler assignment
10cryoSPARC4.7.1final Euler assignment
11cryoSPARC4.7.1classification
12cryoSPARC4.7.13D reconstruction
19Coot0.8.9.3model refinement
20PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 790000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107133 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3JBU

3jbu


Accession code: 3JBU / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 107.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0061160400
ELECTRON MICROSCOPYf_angle_d0.6229240346
ELECTRON MICROSCOPYf_chiral_restr0.040530754
ELECTRON MICROSCOPYf_plane_restr0.004612599
ELECTRON MICROSCOPYf_dihedral_angle_d15.651175063

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