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- PDB-9gux: 30S-TEC (TEC in expressome position) Inactive state 1 -

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Basic information

Entry
Database: PDB / ID: 9gux
Title30S-TEC (TEC in expressome position) Inactive state 1
Components
  • (30S ribosomal protein ...) x 17
  • (DNA-directed RNA polymerase subunit ...) x 4
  • (Small ribosomal subunit protein ...) x 4
  • 16S ribosomal RNA
  • Non-Template DNA strand
  • Template DNA strand
  • Transcription termination/antitermination protein NusG
  • mRNA
KeywordsRIBOSOME / Transcription / translation / coupling
Function / homology
Function and homology information


positive regulation of cytoplasmic translation / RNA polymerase complex / transcription elongation-coupled chromatin remodeling / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding ...positive regulation of cytoplasmic translation / RNA polymerase complex / transcription elongation-coupled chromatin remodeling / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / cytosolic DNA-directed RNA polymerase complex / misfolded RNA binding / Group I intron splicing / RNA folding / bacterial-type flagellum-dependent cell motility / nitrate assimilation / negative regulation of cytoplasmic translation / four-way junction DNA binding / regulation of mRNA stability / DNA-directed RNA polymerase complex / positive regulation of RNA splicing / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / transcription antitermination / DNA-templated transcription initiation / cell motility / DNA-templated transcription termination / maintenance of translational fidelity / ribonucleoside binding / mRNA 5'-UTR binding / : / : / : / : / : / : / DNA-directed RNA polymerase / regulation of translation / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / response to heat / small ribosomal subunit / protein-containing complex assembly / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / intracellular iron ion homeostasis / cytoplasmic translation / tRNA binding / single-stranded RNA binding / protein dimerization activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / Ribosomal protein S1 / : / Ribosomal protein S1-like / 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 ...: / Ribosomal protein S1 / : / Ribosomal protein S1-like / 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 / S1 domain profile. / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / 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 S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6, plastid/chloroplast / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / Ribosomal protein S16 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / Ribosomal protein S16 domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S18
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 ...: / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / 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 uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / Small ribosomal subunit protein uS15 / Transcription termination/antitermination protein NusG / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS1 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsRahil, H. / Weixlbaumer, A. / Webster, M.W.
Funding supportEuropean Union, France, United States, United Kingdom, 6items
OrganizationGrant numberCountry
European Research Council (ERC)679734European Union
Agence Nationale de la Recherche (ANR)ANR-10-LABX-0030-INRT France
Agence Nationale de la Recherche (ANR)ANR-10-IDEX-0002-02 France
European Molecular Biology Organization (EMBO)European Union
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131922 United States
Wellcome Trust203149 United Kingdom
CitationJournal: Science / Year: 2024
Title: Molecular basis of mRNA delivery to the bacterial ribosome.
Authors: Michael W Webster / Adrien Chauvier / Huma Rahil / Andrea Graziadei / Kristine Charles / Nataliya Miropolskaya / Maria Takacs / Charlotte Saint-André / Juri Rappsilber / Nils G Walter / Albert Weixlbaumer /
Abstract: Protein synthesis begins with the formation of a ribosome-messenger RNA (mRNA) complex. In bacteria, the small ribosomal subunit (30) is recruited to many mRNAs through base pairing with the Shine- ...Protein synthesis begins with the formation of a ribosome-messenger RNA (mRNA) complex. In bacteria, the small ribosomal subunit (30) is recruited to many mRNAs through base pairing with the Shine-Dalgarno (SD) sequence and RNA binding by ribosomal protein bS1. Translation can initiate on nascent mRNAs, and RNA polymerase (RNAP) can promote the recruitment of the pioneering 30. Here, we examined 30 recruitment to nascent mRNAs using cryo-electron microscopy, single-molecule fluorescence colocalization, and in-cell cross-linking mass spectrometry. We show that bS1 delivers the mRNA to the ribosome for SD duplex formation and 30 activation. Additionally, bS1 and RNAP stimulate translation initiation. Our work provides a mechanistic framework for how the SD duplex, ribosomal proteins, and RNAP cooperate in 30 recruitment to mRNAs and establish transcription-translation coupling.
History
DepositionSep 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S ribosomal RNA
B: 30S ribosomal protein S1
C: 30S ribosomal protein S2
D: Small ribosomal subunit protein uS3
E: Small ribosomal subunit protein uS4
F: 30S ribosomal protein S5
G: Small ribosomal subunit protein bS6
H: 30S ribosomal protein S7
I: 30S ribosomal protein S8
J: 30S ribosomal protein S9
K: 30S ribosomal protein S10
L: 30S ribosomal protein S11
M: 30S ribosomal protein S12
N: 30S ribosomal protein S13
O: 30S ribosomal protein S14
P: Small ribosomal subunit protein uS15
Q: 30S ribosomal protein S16
R: 30S ribosomal protein S17
S: 30S ribosomal protein S18
T: 30S ribosomal protein S19
U: 30S ribosomal protein S20
V: 30S ribosomal protein S21
X: mRNA
1: DNA-directed RNA polymerase subunit alpha
2: DNA-directed RNA polymerase subunit alpha
3: DNA-directed RNA polymerase subunit beta
4: DNA-directed RNA polymerase subunit beta'
5: DNA-directed RNA polymerase subunit omega
Z: Transcription termination/antitermination protein NusG
6: Non-Template DNA strand
7: Template DNA strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,300,742165
Polymers1,297,40331
Non-polymers3,339134
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules AX

#1: RNA chain 16S ribosomal RNA


Mass: 499778.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli K-12 (bacteria) / References: GenBank: 1929590828
#23: RNA chain mRNA


Mass: 17060.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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30S ribosomal protein ... , 17 types, 17 molecules BCFHIJKLMNOQRSTUV

#2: Protein 30S ribosomal protein S1 / Bacteriophage Q beta RNA-directed RNA polymerase subunit I / Small ribosomal subunit protein bS1


Mass: 61238.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsA, ssyF, b0911, JW0894 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AG67
#3: 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 K-12 (bacteria) / Gene: rpsB, b0169, JW0164 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7V0
#6: Protein 30S ribosomal protein S5 / Small ribosomal subunit protein uS5


Mass: 16532.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsE, spc, b3303, JW3265 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7W1
#8: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 17637.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsG, b3341, JW3303 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P02359
#9: 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 K-12 (bacteria) / Gene: rpsH, b3306, JW3268 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7W7
#10: 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 K-12 (bacteria) / Gene: rpsI, b3230, JW3199 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7X3
#11: 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 K-12 (bacteria) / Gene: rpsJ, nusE, b3321, JW3283 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7R5
#12: Protein 30S ribosomal protein S11 / Small ribosomal subunit protein uS11


Mass: 13870.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsK, b3297, JW3259 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7R9
#13: Protein 30S ribosomal protein S12 / Small ribosomal subunit protein uS12


Mass: 13814.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsL, strA, b3342, JW3304 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7S3
#14: 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 K-12 (bacteria) / Gene: rpsM, b3298, JW3260 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7S9
#15: 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 K-12 (bacteria) / Gene: rpsN, b3307, JW3269 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AG59
#17: 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 K-12 (bacteria) / Gene: rpsP, b2609, JW2590 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7T3
#18: 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 K-12 (bacteria) / Gene: rpsQ, neaA, b3311, JW3273 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AG63
#19: 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 K-12 (bacteria) / Gene: rpsR, b4202, JW4160 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7T7
#20: 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 K-12 (bacteria) / Gene: rpsS, b3316, JW3278 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7U3
#21: 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 K-12 (bacteria) / Gene: rpsT, b0023, JW0022 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7U7
#22: 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 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 ... , 4 types, 4 molecules DEGP

#4: Protein 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 K-12 (bacteria)
Gene: rpsC, A5U30_004548, A8502_004027, ACN81_25500, ACU57_20980, AW118_24880, AWP47_12665, B6R15_004073, B6R31_004972, BANRA_01945, BANRA_04324, BCB93_004289, BE932_15515, BER14_25170, BG944_001129, ...Gene: rpsC, A5U30_004548, A8502_004027, ACN81_25500, ACU57_20980, AW118_24880, AWP47_12665, B6R15_004073, B6R31_004972, BANRA_01945, BANRA_04324, BCB93_004289, BE932_15515, BER14_25170, BG944_001129, BGM66_003597, BGZ_02594, BGZ_04121, BJI68_08695, BK292_20485, BK383_24665, BKL28_004547, BR158_003786, BTB68_004360, BTQ06_10670, BvCmsKKP061_03026, BvCmsSIP010_02681, BXT93_05495, C0P57_002664, C1Q91_004908, C2121_004166, C2M16_25425, C2R31_004629, C3F40_19740, C9Z68_22615, CF22_004853, CG704_20890, CIG67_10695, CQ842_14345, CQ842_22325, CTR35_003626, CV83915_02784, D3C88_13310, D3G36_23070, D4M65_20635, D4N09_20235, D9D43_22570, D9E49_05220, D9J61_16715, DD762_23610, DIV22_15195, DNQ45_03820, DNX30_25415, DS732_24325, DTL43_20935, DU321_12065, E2865_04467, E4K51_21555, E5H86_24460, E6D34_21695, EAI46_07540, ECs4179, EIA08_24020, EIZ93_12405, EN85_004353, EPS76_07150, EPS97_20030, EWK56_25060, ExPECSC038_03644, F7F11_22660, F7N46_23945, F9413_21170, F9461_25590, F9B07_24620, FGAF848_25890, FIJ20_21130, FJQ40_18370, FKO60_25700, FOI11_019195, FOI11_03985, FPI65_20370, FPS11_25365, FVB16_04935, FWK02_12630, FZU14_21885, G3V95_19910, G3W53_21020, G4A38_21575, G4A47_20845, G5603_24650, GAI89_24765, GAJ12_24655, GFY48_21635, GGB84_004455, GKF66_21610, GNW61_16695, GNZ05_25920, GOP25_22770, GP711_23370, GP954_00880, GP965_04360, GP975_01250, GP979_01940, GQA06_03885, GQE86_20145, GQM04_10630, GQM13_25265, GQM21_11295, GQN34_23330, GQW07_21485, GRO95_20750, GRW05_09125, GRW24_04690, GUC01_21245, H0O53_20765, H0O72_19480, HEP30_018700, HEP34_004758, HHH44_004523, HI055_004152, HIE29_005199, HJQ60_004999, HLX92_10010, HLZ50_22115, HMV95_19670, HMW38_23170, HV109_02125, HV209_14650, HVV39_09330, HVW04_17470, HVW43_18605, HVY77_02110, I6H00_20860, I6H02_12055, J0541_004409, J5U05_004075, JNP96_25370, NCTC10082_02827, NCTC10089_00490, NCTC10429_01082, NCTC10764_03851, NCTC10767_01504, NCTC10974_00537, NCTC11126_02758, NCTC11181_02726, NCTC11341_01901, NCTC7922_04054, NCTC7927_00539, NCTC7928_02529, NCTC8009_01498, NCTC8179_05929, NCTC8333_00477, NCTC8500_00322, NCTC8621_00496, NCTC8622_00518, NCTC8959_03273, NCTC8960_03058, NCTC9001_04242, NCTC9045_00553, NCTC9075_00712, NCTC9077_00592, NCTC9081_00905, NCTC9117_00744, NCTC9702_00525, NCTC9706_02725, NCTC9962_06785, OGM49_22395, P6223_003995, QDW62_02130, RZR61_12955, SAMEA3472112_00681, SAMEA3752557_01964, WR15_19670
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: C3SQX2
#5: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsD, BWG_2987 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: C4ZUF1
#7: Protein Small ribosomal subunit protein bS6


Mass: 15197.032 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria)
Gene: rpsF, BANRA_02890, BGM66_001638, BJI68_10200, C0P57_000210, CIG67_23060, CTR35_001516, CV83915_01828, E6D34_03615, G4A38_03220, G4A47_10770, GNW61_00195, GQM21_23655, GRW05_28450, HVY77_22975, ...Gene: rpsF, BANRA_02890, BGM66_001638, BJI68_10200, C0P57_000210, CIG67_23060, CTR35_001516, CV83915_01828, E6D34_03615, G4A38_03220, G4A47_10770, GNW61_00195, GQM21_23655, GRW05_28450, HVY77_22975, J0541_002297, JNP96_03175, NCTC8500_05020, NCTC9045_05184, NCTC9706_01764, P6223_000651, SAMEA3752557_01699
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: W8T6F0
#16: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpsO, secC, b3165, JW3134 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ADZ4

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules 12345

#24: Protein DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 36558.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#25: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150820.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria)
Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A8V2, DNA-directed RNA polymerase
#26: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 155237.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpoC, Z5561, ECs4911 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A8T8, DNA-directed RNA polymerase
#27: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10249.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rpoZ, b3649, JW3624 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A800, DNA-directed RNA polymerase

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Protein , 1 types, 1 molecules Z

#28: Protein Transcription termination/antitermination protein NusG


Mass: 20431.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: nusG, b3982, JW3945 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0AFG0

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DNA chain , 2 types, 2 molecules 67

#29: DNA chain Non-Template DNA strand


Mass: 11759.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#30: DNA chain Template DNA strand


Mass: 11890.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 134 molecules

#31: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 132 / Source method: obtained synthetically / Formula: Mg
#32: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
130S ribosomal subunit boud to TECRIBOSOME#1-#300RECOMBINANT
2TECCOMPLEX#23-#301RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli K-12 (bacteria)83333
32Escherichia coli K-12 (bacteria)83333
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli K-12 (bacteria)83333
32Escherichia coli K-12 (bacteria)83333
Buffer solutionpH: 7.4
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 49.95 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11965 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00785919
ELECTRON MICROSCOPYf_angle_d0.859123848
ELECTRON MICROSCOPYf_dihedral_angle_d13.21448396
ELECTRON MICROSCOPYf_chiral_restr0.05915176
ELECTRON MICROSCOPYf_plane_restr0.0069997

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