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- PDB-9n2c: Impacts of ribosomal RNA sequence variation on gene expression an... -

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Basic information

Entry
Database: PDB / ID: 9n2c
TitleImpacts of ribosomal RNA sequence variation on gene expression and phenotype: Cryo-EM structure of the rrsH ribosome (HBB-70S)
Components
  • (30S ribosomal protein ...) x 18
  • (50S ribosomal protein ...) x 26
  • (Large ribosomal subunit protein ...) x 3
  • (Small ribosomal subunit protein ...) x 2
  • 16S ribosomal RNA (rRNA) from the rrnH operon
  • 23S ribosomal RNA (rRNA) from the rrnB operon
  • 5S large subunit ribosomal RNA of the H operon
  • N-formyl-methionine initiator tRNA (fMet-tRNAfMet)
  • Synthetic messenger RNA (mRNA) 60 bp in length
KeywordsRIBOSOME / Translation / Transcription / rDNA / rRNA / Cryo-EM
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / regulation of mRNA stability / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / ribosome assembly / transcription elongation factor complex / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / response to reactive oxygen species / DNA endonuclease activity / transcription antitermination / translational initiation / regulation of cell growth / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosome biogenesis / regulation of translation / large ribosomal subunit / transferase activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / 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 / 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 L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 signature. ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / : / Ribosomal protein 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 L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein 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 L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / N-FORMYLMETHIONINE / : / 1,4-DIAMINOBUTANE / SPERMIDINE / : / : / : / RNA / RNA (> 10) ...ADENOSINE-5'-TRIPHOSPHATE / N-FORMYLMETHIONINE / : / 1,4-DIAMINOBUTANE / SPERMIDINE / : / : / : / 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 K-12 (bacteria)
Escherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsWelfer, G.A. / Brady, R.A. / Natchiar, S.K. / Watson, Z.L. / Rundlet, E.J. / Alejo, J.L. / Singh, A.P. / Mishra, N.K. / Altman, R.B. / Blanchard, S.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Philos Trans R Soc Lond B Biol Sci / Year: 2025
Title: Impacts of ribosomal RNA sequence variation on gene expression and phenotype.
Authors: Griffin A Welfer / Ryan A Brady / S Kundhavai Natchiar / Zoe L Watson / Emily J Rundlet / Jose L Alejo / Anand P Singh / Nitish K Mishra / Roger B Altman / Scott C Blanchard /
Abstract: Since the framing of the Central Dogma, it has been speculated that physically distinct ribosomes within cells may influence gene expression and cellular physiology. While heterogeneity in ribosome ...Since the framing of the Central Dogma, it has been speculated that physically distinct ribosomes within cells may influence gene expression and cellular physiology. While heterogeneity in ribosome composition has been reported in bacteria, protozoans, fungi, zebrafish, mice and humans, its functional implications remain actively debated. Here, we review recent evidence demonstrating that expression of conserved variant ribosomal DNA (rDNA) alleles in bacteria, mice and humans renders their actively translating ribosome pool intrinsically heterogeneous at the level of ribosomal RNA (rRNA). In this context, we discuss reports that nutrient limitation-induced stress in leads to changes in variant rRNA allele expression, programmatically altering transcription and cellular phenotype. We highlight that cells expressing ribosomes from distinct operons exhibit distinct drug sensitivities, which can be recapitulated and potentially rationalized by subtle perturbations in ribosome structure or in their dynamic properties. Finally, we discuss evidence that differential expression of variant rDNA alleles results in different populations of ribosome subtypes within mammalian tissues. These findings motivate further research into the impacts of rRNA heterogeneities on ribosomal function and predict that strategies targeting distinct ribosome subtypes may hold therapeutic potential.This article is part of the discussion meeting issue 'Ribosome diversity and its impact on protein synthesis, development and disease'.
#1: Journal: Cell Rep / Year: 2018
Title: Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype.
Authors: Chad M Kurylo / Matthew M Parks / Manuel F Juette / Boris Zinshteyn / Roger B Altman / Jordana K Thibado / C Theresa Vincent / Scott C Blanchard /
Abstract: Prevailing dogma holds that ribosomes are uniform in composition and function. Here, we show that nutrient limitation-induced stress in E. coli changes the relative expression of rDNA operons to ...Prevailing dogma holds that ribosomes are uniform in composition and function. Here, we show that nutrient limitation-induced stress in E. coli changes the relative expression of rDNA operons to alter the rRNA composition within the actively translating ribosome pool. The most upregulated operon encodes the unique 16S rRNA, rrsH, distinguished by conserved sequence variation within the small ribosomal subunit. rrsH-bearing ribosomes affect the expression of functionally coherent gene sets and alter the levels of the RpoS sigma factor, the master regulator of the general stress response. These impacts are associated with phenotypic changes in antibiotic sensitivity, biofilm formation, and cell motility and are regulated by stress response proteins, RelA and RelE, as well as the metabolic enzyme and virulence-associated protein, AdhE. These findings establish that endogenously encoded, naturally occurring rRNA sequence variation can modulate ribosome function, central aspects of gene expression regulation, and cellular physiology.
History
DepositionJan 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
16: 16S ribosomal RNA (rRNA) from the rrnH operon
SB: 30S ribosomal protein S2
SC: 30S ribosomal protein S3
SD: 30S ribosomal protein S4
SE: 30S ribosomal protein S5
SF: 30S ribosomal protein S6
SG: 30S ribosomal protein S7
SH: 30S ribosomal protein S8
SI: 30S ribosomal protein S9
SJ: 30S ribosomal protein S10
SK: Small ribosomal subunit protein uS11
SL: Small ribosomal subunit protein uS12
SM: 30S ribosomal protein S13
SN: 30S ribosomal protein S14
SO: 30S ribosomal protein S15
SP: 30S ribosomal protein S16
SQ: 30S ribosomal protein S17
SR: 30S ribosomal protein S18
SS: 30S ribosomal protein S19
ST: 30S ribosomal protein S20
SU: 30S ribosomal protein S21
mR: Synthetic messenger RNA (mRNA) 60 bp in length
23: 23S ribosomal RNA (rRNA) from the rrnB operon
5: 5S large subunit ribosomal RNA of the H operon
LB: 50S ribosomal protein L2
LC: 50S ribosomal protein L3
LD: Large ribosomal subunit protein uL4
LE: 50S ribosomal protein L5
LF: 50S ribosomal protein L6
LI: 50S ribosomal protein L9
LM: 50S ribosomal protein L13
LN: 50S ribosomal protein L14
LO: 50S ribosomal protein L15
LP: 50S ribosomal protein L16
LQ: 50S ribosomal protein L17
LR: 50S ribosomal protein L18
LS: 50S ribosomal protein L19
LT: 50S ribosomal protein L20
LU: 50S ribosomal protein L21
LV: Large ribosomal subunit protein uL22
LW: 50S ribosomal protein L23
LX: 50S ribosomal protein L24
LY: 50S ribosomal protein L25
La: 50S ribosomal protein L27
Lb: 50S ribosomal protein L28
Lc: 50S ribosomal protein L29
Ld: Large ribosomal subunit protein uL30
Le: 50S ribosomal protein L31
Lf: 50S ribosomal protein L32
Lg: 50S ribosomal protein L33
Lh: 50S ribosomal protein L34
Li: 50S ribosomal protein L35
Lj: 50S ribosomal protein L36
Pt: N-formyl-methionine initiator tRNA (fMet-tRNAfMet)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,196,231407
Polymers2,184,44254
Non-polymers11,790353
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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RNA chain , 5 types, 5 molecules 16mR235Pt

#1: RNA chain 16S ribosomal RNA (rRNA) from the rrnH operon


Mass: 499811.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 16S ribosomal RNA (rRNA) from the rrnH operon / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli K-12 (bacteria) / References: GenBank: 1929590828
#22: RNA chain Synthetic messenger RNA (mRNA) 60 bp in length


Mass: 19128.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic messenger RNA (mRNA) 60 bp in length / Source: (synth.) Escherichia coli BL21 (bacteria)
#23: RNA chain 23S ribosomal RNA (rRNA) from the rrnB operon


Mass: 941811.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 23S ribosomal RNA (rRNA) from the rrnB operon / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli K-12 (bacteria)
#24: RNA chain 5S large subunit ribosomal RNA of the H operon


Mass: 38814.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 5S large subunit ribosomal RNA of the H operon / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli K-12 (bacteria) / References: GenBank: 1789840096
#54: RNA chain N-formyl-methionine initiator tRNA (fMet-tRNAfMet)


Mass: 24848.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-formyl-methionine initiator tRNA (fMet-tRNAfMet) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): MRE600 / References: GenBank: 2696706521

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

#2: 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
Details: Small ribosomal subunit protein uS2 (S2) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsB, b0169, JW0164 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7V0
#3: 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
Details: Small ribosomal subunit protein uS3 (S3) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsC, b3314, JW3276 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7V3
#4: 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
Details: Small ribosomal subunit protein uS4 (S4) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsD, ramA, b3296, JW3258 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7V8
#5: 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
Details: Small ribosomal subunit protein uS5 (S5) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsE, spc, b3303, JW3265 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7W1
#6: Protein 30S ribosomal protein S6 / Small ribosomal subunit protein bS6


Mass: 15727.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Small ribosomal subunit protein bS6 (S6) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsF, b4200, JW4158 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P02358
#7: 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
Details: Small ribosomal subunit protein uS7 (S7) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsG, b3341, JW3303 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P02359
#8: 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
Details: Small ribosomal subunit protein uS8 (S8) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsH, b3306, JW3268 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7W7
#9: 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
Details: Small ribosomal subunit protein uS9 (S9) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsI, b3230, JW3199 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7X3
#10: Protein 30S ribosomal protein S10 / Small ribosomal subunit protein uS10


Mass: 11755.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Small ribosomal subunit protein uS10 (S10) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsJ, nusE, b3321, JW3283 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7R5
#13: 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
Details: Small ribosomal subunit protein uS13 (S13) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsM, b3298, JW3260 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7S9
#14: 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
Details: Small ribosomal subunit protein uS14 (S14) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsN, b3307, JW3269 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AG59
#15: 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
Details: Small ribosomal subunit protein uS15 (S15) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsO, secC, b3165, JW3134 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ADZ4
#16: 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
Details: Small ribosomal subunit protein bS16 (S16) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsP, b2609, JW2590 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7T3
#17: 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
Details: Small ribosomal subunit protein uS17 (S17) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsQ, neaA, b3311, JW3273 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AG63
#18: Protein 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Small ribosomal subunit protein bS18 (S18) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsR, b4202, JW4160 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7T7
#19: Protein 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Small ribosomal subunit protein uS19 (S19) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsS, b3316, JW3278 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7U3
#20: 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
Details: Small ribosomal subunit protein bS20 (S20) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsT, b0023, JW0022 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7U7
#21: 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
Details: Small ribosomal subunit protein bS21 (S21) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsU, b3065, JW3037 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P68679

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

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


Mass: 13871.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Small ribosomal subunit protein uS11 (S11) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsK, b3297, JW3259 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7R9
#12: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13814.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Small ribosomal subunit protein uS12 (S12) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsL, strA, b3342, JW3304 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7S3

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50S ribosomal protein ... , 26 types, 26 molecules LBLCLELFLILMLNLOLPLQLRLSLTLULWLXLYLaLbLcLeLfLgLhLiLj

#25: Protein 50S ribosomal protein L2


Mass: 29923.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein uL2 (L2) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplB, b3317, JW3279 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P60422
#26: 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
Details: Large ribosomal subunit protein uL3 (L3) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplC, b3320, JW3282 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P60438
#28: Protein 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein uL5 (L5) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplE, b3308, JW3270 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P62399
#29: Protein 50S ribosomal protein L6 / Large ribosomal subunit protein uL6


Mass: 18932.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein uL6 (L6) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplF, b3305, JW3267 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AG55
#30: 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
Details: Large ribosomal subunit protein bL9 (L9) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplI, b4203, JW4161 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7R1
#31: 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
Details: Large ribosomal subunit protein uL13 (L13) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplM, b3231, JW3200 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AA10
#32: 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
Details: Large ribosomal subunit protein uL14 (L14) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplN, b3310, JW3272 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ADY3
#33: 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
Details: Large ribosomal subunit protein uL15 (L15) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplO, b3301, JW3263 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P02413
#34: Protein 50S ribosomal protein L16


Mass: 15327.261 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein uL16 (L16) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplP, b3313, JW3275 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ADY7
#35: Protein 50S ribosomal protein L17 / Large ribosomal subunit protein bL17


Mass: 14393.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein bL17 (L17) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplQ, b3294, JW3256 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AG44
#36: Protein 50S ribosomal protein L18 / Large ribosomal subunit protein uL18


Mass: 12794.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein uL18 (L18) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplR, b3304, JW3266 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0C018
#37: Protein 50S ribosomal protein L19 / Large ribosomal subunit protein bL19


Mass: 13159.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein bL19 (L19) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplS, b2606, JW2587 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7K6
#38: Protein 50S ribosomal protein L20 / Large ribosomal subunit protein bL20


Mass: 13528.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein bL20 (L20) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplT, pdzA, b1716, JW1706 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7L3
#39: 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
Details: Large ribosomal subunit protein bL21 (L21) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplU, b3186, JW3153 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AG48
#41: Protein 50S ribosomal protein L23 / Large ribosomal subunit protein uL23


Mass: 11222.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein uL23 (L23) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplW, b3318, JW3280 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ADZ0
#42: 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
Details: Large ribosomal subunit protein uL24 (L24) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplX, b3309, JW3271 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P60624
#43: 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
Details: Large ribosomal subunit protein bL25 (L25) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplY, b2185, JW2173 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P68919
#44: Protein 50S ribosomal protein L27 / Large ribosomal subunit protein bL27


Mass: 9146.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein bL27 (L27) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpmA, b3185, JW3152 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7L8
#45: Protein 50S ribosomal protein L28 / Large ribosomal subunit protein bL28


Mass: 9027.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein bL28 (L28) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpmB, b3637, JW3612 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7M2
#46: Protein 50S ribosomal protein L29 / Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein uL29 (L29) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpmC, b3312, JW3274 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7M6
#48: Protein 50S ribosomal protein L31 / Large ribosomal subunit protein bL31-A


Mass: 7887.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein bL31 (L31) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpmE, b3936, JW3907 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7M9
#49: Protein 50S ribosomal protein L32 / Large ribosomal subunit protein bL32


Mass: 6463.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein bL32 (L32) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpmF, b1089, JW1075 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7N4
#50: Protein 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein bL33 (L33) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpmG, b3636, JW3611 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7N9
#51: 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
Details: Large ribosomal subunit protein bL34 (L34) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpmH, rimA, ssaF, b3703, JW3680 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7P5
#52: Protein 50S ribosomal protein L35 / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein bL35 (L35) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpmI, b1717, JW1707 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7Q1
#53: 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
Details: Large ribosomal subunit protein bL36A (L36) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpmJ, b3299, JW3261 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7Q6

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Large ribosomal subunit protein ... , 3 types, 3 molecules LDLVLd

#27: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein uL4 (L4) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplD, eryA, b3319, JW3281 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P60723
#40: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Large ribosomal subunit protein uL22 (L22) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rplV, eryB, b3315, JW3277 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P61175
#47: 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
Details: Large ribosomal subunit protein uL30 (L30) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpmD, b3302, JW3264 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AG51

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Non-polymers , 7 types, 353 molecules

#55: Chemical
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H12N2
#56: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H19N3
#57: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 283 / Source method: obtained synthetically / Formula: Mg
#58: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: K
#59: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#60: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#61: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S

-
Details

Has ligand of interestY
Has protein modificationY

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Experimental details

-
Experiment

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

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Sample preparation

ComponentName: 70S Ribosome initiation complex (Delta7prrn-HBB 70S) / Type: RIBOSOME / Entity ID: #1-#54 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283.15 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 300 nm
Image recordingAverage exposure time: 3 sec. / Electron dose: 1.45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM softwareName: PHENIX / Version: 1.21_5190: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 417599 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 7N1P

7n1p


Accession code: 7N1P / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005159074
ELECTRON MICROSCOPYf_angle_d0.931237890
ELECTRON MICROSCOPYf_dihedral_angle_d22.05675821
ELECTRON MICROSCOPYf_chiral_restr0.05430335
ELECTRON MICROSCOPYf_plane_restr0.00812757

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