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- PDB-9y79: Escherichia coli transcription-translation loosely coupled comple... -

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Basic information

Entry
Database: PDB / ID: 9y79
TitleEscherichia coli transcription-translation loosely coupled complex (TTC-LC^walked) containing mRNA with a 39 nt long spacer, NusG, NusA, and fMet-tRNAs in E-site and P-site
Components
  • (30S ribosomal protein ...) x 4
  • (50S ribosomal protein ...) x 18
  • (DNA-directed RNA polymerase subunit ...) x 4
  • (Large ribosomal subunit protein ...) x 13
  • (Small ribosomal subunit protein ...) x 17
  • (Transcription termination/antitermination protein ...) x 2
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • E-site and P-site tRNA (fMet)
  • NT DNA
  • Ribosomal protein L21
  • T DNA
  • mRNA with 39 nt long spacer
KeywordsTRANSCRIPTION / TRANSLATION / RIBOSOME/TRANSFERASE/DNA/RNA / Transcription-translation coupled complex / RIBOSOME-TRANSFERASE-DNA-RNA complex
Function / homology
Function and homology information


stringent response / RNA polymerase complex / DNA-templated transcription elongation / negative regulation of cytoplasmic translational initiation / 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 / cytosolic DNA-directed RNA polymerase complex ...stringent response / RNA polymerase complex / DNA-templated transcription elongation / negative regulation of cytoplasmic translational initiation / 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 / cytosolic DNA-directed RNA polymerase complex / misfolded RNA binding / Group I intron splicing / RNA folding / bacterial-type flagellum-dependent cell motility / nitrate assimilation / translational termination / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / regulation of DNA-templated transcription elongation / transcription elongation factor complex / cytosolic ribosome assembly / ribosome assembly / assembly of large subunit precursor of preribosome / DNA-directed RNA polymerase complex / cell motility / transcription antitermination / regulation of cell growth / DNA-templated transcription initiation / translational initiation / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / large ribosomal subunit / response to heat / transferase activity / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / protein-containing complex assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / intracellular iron ion homeostasis / cytoplasmic translation / tRNA binding / protein dimerization activity / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / DNA-binding transcription factor activity / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / nucleotide binding / mRNA binding / magnesium ion binding / DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / : / NusA-like second KH domain / Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like first KH domain ...: / : / NusA-like second KH domain / Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like first KH domain / Transcription termination/antitermination protein NusA, bacterial / Ribosomal protein S1 / Ribosomal protein S1-like / : / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / NusG-like / Transcription termination factor nusG / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / Type-1 KH domain profile. / NusG, N-terminal domain superfamily / DNA repair Rad51/transcription factor NusA, alpha-helical / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / SAM-like Helix-hairpin-helix tandem / Ribosomal protein L10 / : / S1 domain profile. / Ribosomal protein L11, bacterial-type / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / 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 beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein S21 / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / : / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L28/L24 superfamily
Similarity search - Domain/homology
: / : / : / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...: / : / : / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL12 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL21 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Transcription termination/antitermination protein NusA / Transcription termination/antitermination protein NusG / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein bS1 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsShandilya, S. / Wang, C. / Molodtsov, V. / Ebright, R.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM041376 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural basis of long-range transcription-translation coupling.
Authors: Chengyuan Wang / Vadim Molodtsov / Shashank Shandilya / Linlin You / Jing Zhang / Konstantin Kuznedelov / Bryce E Nickels / Jason T Kaelber / Gregor Blaha / Richard H Ebright /
Abstract: Structures recently have been reported of molecular assemblies that mediate transcription-translation coupling in . In these molecular assemblies, termed "coupled transcription-translation complexes" ...Structures recently have been reported of molecular assemblies that mediate transcription-translation coupling in . In these molecular assemblies, termed "coupled transcription-translation complexes" or "TTC-B," RNA polymerase (RNAP) directly interacts with the ribosome, the transcription elongation factor NusG or its paralog RfaH forms a bridge between RNAP and ribosome, and the transcription elongation factor NusA optionally forms a second bridge between RNAP and ribosome. Here, we report structures of coupled transcription-translation complexes having mRNA spacers between RNAP and ribosome longer than the maximum-length mRNA spacer compatible with formation of TTC-B. The results define a class of coupled transcription-translation complex, termed "TTC-LC," where "LC" denotes "long-range coupling." TTC-LC differs from TTC-B by a ~60° rotation and ~70 Å translation of RNAP relative to ribosome, resulting in loss of direct interactions between RNAP and ribosome and creation of a ~70 Å gap between RNAP and ribosome. TTC-LC accommodates long mRNA spacers by looping out mRNA from the gap between RNAP and ribosome. We present evidence that TTC-LC is a functional intermediate in assembling and disassembling TTC-B, mediating pre-TTC-B transcription-translation coupling before a ribosome catches up to RNAP, and mediating post-TTC-B transcription-translation coupling after a ribosome stops moving and RNAP continues moving. We show that TTC-B, but not TTC-LC, is severely defective in RNA-hairpin-dependent transcription termination, and that both TTC-B and TTC-LC are severely defective in Rho-dependent transcription termination.
History
DepositionSep 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Ribosomal protein L21
1: 50S ribosomal protein L22
2: 50S ribosomal protein L23
3: 50S ribosomal protein L24
4: Large ribosomal subunit protein bL25
5: NT DNA
6: T DNA
7: mRNA with 39 nt long spacer
9: 50S ribosomal protein L10
A: E-site and P-site tRNA (fMet)
AA: DNA-directed RNA polymerase subunit beta
AC: DNA-directed RNA polymerase subunit alpha
AD: DNA-directed RNA polymerase subunit alpha
AE: DNA-directed RNA polymerase subunit beta'
AF: DNA-directed RNA polymerase subunit omega
AG: Transcription termination/antitermination protein NusA
B: E-site and P-site tRNA (fMet)
C: Small ribosomal subunit protein bS18
D: 16S rRNA
E: Small ribosomal subunit protein bS20
F: Small ribosomal subunit protein bS21
G: 30S ribosomal protein S2
H: Small ribosomal subunit protein bS1
I: 30S ribosomal protein S3
J: Small ribosomal subunit protein uS4
K: Small ribosomal subunit protein uS5
L: Small ribosomal subunit protein bS6
M: Small ribosomal subunit protein uS7
N: Small ribosomal subunit protein uS8
NG: Transcription termination/antitermination protein NusG
O: Small ribosomal subunit protein uS9
P: Small ribosomal subunit protein uS10
Q: 30S ribosomal protein S11
R: 30S ribosomal protein S12
S: Small ribosomal subunit protein uS14
T: Small ribosomal subunit protein uS15
U: Small ribosomal subunit protein bS16
V: Small ribosomal subunit protein uS17
W: Small ribosomal subunit protein uS19
X: Small ribosomal subunit protein uS13
Y: 50S ribosomal protein L11
Z: Large ribosomal subunit protein bL12
a: 23S rRNA
b: 50S ribosomal protein L27
c: 50S ribosomal protein L28
d: 5S rRNA
e: Large ribosomal subunit protein uL29
f: 50S ribosomal protein L30
g: 50S ribosomal protein L31
h: 50S ribosomal protein L2
i: 50S ribosomal protein L32
j: 50S ribosomal protein L3
k: 50S ribosomal protein L33
l: Large ribosomal subunit protein uL4
m: 50S ribosomal protein L34
n: Large ribosomal subunit protein uL5
o: 50S ribosomal protein L35
p: Large ribosomal subunit protein uL6
q: 50S ribosomal protein L36
r: Large ribosomal subunit protein bL9
s: Large ribosomal subunit protein uL13
t: Large ribosomal subunit protein uL14
u: Large ribosomal subunit protein uL15
v: 50S ribosomal protein L16
w: Large ribosomal subunit protein bL17
x: Large ribosomal subunit protein uL18
y: Large ribosomal subunit protein bL19
z: 50S ribosomal protein L20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,808,92071
Polymers2,808,76568
Non-polymers1553
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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Protein , 1 types, 1 molecules 0

#1: Protein Ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SSG2

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50S ribosomal protein ... , 18 types, 18 molecules 1239Ybcfghijkmoqvz

#2: Protein 50S ribosomal protein L22 / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P61175
#3: Protein 50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQV2
#4: Protein 50S ribosomal protein L24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQZ7
#9: Protein 50S ribosomal protein L10 / 50S ribosomal protein L8 / Large ribosomal subunit protein uL10


Mass: 17736.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J3
#39: Protein 50S ribosomal protein L11 / Large ribosomal subunit protein uL11


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J7
#42: Protein 50S ribosomal protein L27 / Large ribosomal subunit protein bL27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#43: Protein 50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A1X3JA73
#46: Protein 50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR32
#47: Protein 50S ribosomal protein L31 / Large ribosomal subunit protein bL31-A


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M9
#48: Protein 50S ribosomal protein L2 / Large ribosomal subunit protein uL2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60422
#49: Protein 50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3TE02
#50: Protein 50S ribosomal protein L3 / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#51: Protein 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SME7
#53: Protein/peptide 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MGC4
#55: 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 natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#57: Protein/peptide 50S ribosomal protein L36


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0E2L017
#62: Protein 50S ribosomal protein L16 / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7
#66: Protein 50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MAS6

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Large ribosomal subunit protein ... , 13 types, 13 molecules 4Zelnprstuwxy

#5: Protein Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919
#40: Protein Large ribosomal subunit protein bL12


Mass: 12309.155 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SIB2
#45: Protein Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQY2
#52: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60723
#54: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P62399
#56: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#58: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R1
#59: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA10
#60: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3
#61: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02413
#63: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#64: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#65: Protein Large ribosomal subunit protein bL19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K8

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DNA chain , 2 types, 2 molecules 56

#6: DNA chain NT DNA


Mass: 15464.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain T DNA


Mass: 15340.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain , 5 types, 6 molecules 7ABDad

#8: RNA chain mRNA with 39 nt long spacer


Mass: 17658.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#10: RNA chain E-site and P-site tRNA (fMet)


Mass: 24496.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: GenBank: 1870104878
#17: RNA chain 16S rRNA


Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1732209707
#41: RNA chain 23S rRNA


Mass: 941635.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 937521852
#44: RNA chain 5S rRNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1273279017

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

#11: 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 (E. coli)
Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0A8V2, DNA-directed RNA polymerase
#12: 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 (E. coli) / Gene: rpoA, pez, phs, sez, b3295, JW3257
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#13: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 155366.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, tabB, b3988, JW3951
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0A8T7, DNA-directed RNA polymerase
#14: 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 (E. coli) / Gene: rpoZ, b3649, JW3624
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0A800, DNA-directed RNA polymerase

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Transcription termination/antitermination protein ... , 2 types, 2 molecules AGNG

#15: Protein Transcription termination/antitermination protein NusA


Mass: 54932.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nusA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0AFF8
#28: Protein Transcription termination/antitermination protein NusG


Mass: 20560.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nusG, Z5555, ECs4905
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0AFG1

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Small ribosomal subunit protein ... , 17 types, 17 molecules CEFHJKLMNOPSTUVWX

#16: Protein Small ribosomal subunit protein bS18


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0E2KXL3
#18: Protein Small ribosomal subunit protein bS20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3TRH7
#19: Protein Small ribosomal subunit protein bS21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0E2L2J1
#21: Protein Small ribosomal subunit protein bS1 / 30S ribosomal protein S1


Mass: 61238.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG69
#23: Protein Small ribosomal subunit protein uS4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8
#24: Protein Small ribosomal subunit protein uS5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W1
#25: Protein Small ribosomal subunit protein bS6


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#26: Protein Small ribosomal subunit protein uS7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#27: Protein Small ribosomal subunit protein uS8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR12
#29: Protein Small ribosomal subunit protein uS9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SRY2
#30: Protein Small ribosomal subunit protein uS10


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQT7
#33: Protein Small ribosomal subunit protein uS14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A2X1PQW4
#34: Protein Small ribosomal subunit protein uS15


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SSQ7
#35: Protein Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SYP2
#36: Protein Small ribosomal subunit protein uS17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQY7
#37: Protein Small ribosomal subunit protein uS19


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQW2
#38: Protein Small ribosomal subunit protein uS13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A7U9IV78

+
30S ribosomal protein ... , 4 types, 4 molecules GIQR

#20: Protein 30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3TPN2
#22: Protein 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3
#31: Protein 30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCR3
#32: Protein 30S ribosomal protein S12


Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3

+
Non-polymers , 2 types, 3 molecules

#67: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#68: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

-
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: Transcription-Translation coupled complex / Type: COMPLEX
Entity ID: #7, #1-#5, #9-#10, #16-#27, #29-#66, #6, #8, #11, #28, #12-#15
Source: MULTIPLE SOURCES
Molecular weightValue: 2.8 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
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 magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2UCSF ChimeraX1.9/v10model fitting
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 592698
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31000 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8VOQ

8voq


Accession code: 8VOQ / Source name: PDB / Type: experimental model

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