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- PDB-8y5k: E.coli transcription translation coupling complex in TTC-A state ... -

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Open data

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Basic information

Entry

Database: PDB / ID: 8y5k

Title

E.coli transcription translation coupling complex in TTC-A state 2 containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin

Components

(30S ribosomal protein ...) x 20
(50S ribosomal protein ...) x 30
(DNA-directed RNA polymerase subunit ...) x 4
16S rRNA
23S rRNA
5S rRNA
Elongation factor G
Large ribosomal subunit protein uL1
Transcription termination/antitermination protein NusG
Viomycin
mRNA
non-templete DNA strand
tRNA(Phe)
tRNA(fMet)
templete DNA strand

Keywords

RIBOSOME / RNA polymerase / translation / transcription / coupling / transcription-translation coupling / expressome

Function / homology

Function and homology information

ribosome disassembly / guanosine tetraphosphate binding / RNA polymerase complex / negative regulation of cytoplasmic translational initiation / transcription elongation-coupled chromatin remodeling / submerged biofilm formation / stringent response / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly ...ribosome disassembly / guanosine tetraphosphate binding / RNA polymerase complex / negative regulation of cytoplasmic translational initiation / transcription elongation-coupled chromatin remodeling / submerged biofilm formation / stringent response / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / misfolded RNA binding / Group I intron splicing / translational elongation / RNA folding / bacterial-type flagellum-dependent cell motility / transcriptional attenuation / translation elongation factor activity / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / nitrate assimilation / translational termination / 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 / DNA-templated transcription initiation / cell motility / regulation of cell growth / 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 / ribosome biogenesis / large ribosomal subunit / regulation of translation / transferase activity / ribosome binding / response to heat / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / protein-containing complex assembly / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / GTPase activity / GTP binding / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function

: / Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / NusG-like / Transcription termination factor nusG ...: / Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / Ribosomal protein L1, bacterial-type / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / DNA-directed RNA polymerase, omega subunit / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / 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 / Elongation factor Tu domain 2 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L11, bacterial-type / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / 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 L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L17 signature. / 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 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
Similarity search - Domain/homology

Viomycin / GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / : / : / : / : / DNA / DNA (> 10) / polypeptide(D) ...Viomycin / GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / : / : / : / : / DNA / DNA (> 10) / polypeptide(D) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Elongation factor G / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / 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 / 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 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Transcription termination/antitermination protein NusG / 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 species

Escherichia coli K-12 (bacteria)
synthetic construct (others)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.9 Å

Authors

Zhang, J. / Lu, G. / Wang, C. / Lin, J.

Funding support

China, 2items

Citation

Journal: To be published
Title: E.coli transcription translation coupling complex in TTC-A state 2 containing mRNA with 27-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin
Authors: Zhang, J. / Lu, G. / Ebright, R.H. / Lin, J. / Wang, C.

History

Deposition	Jan 31, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 13, 2025	Provider: repository / Type: Initial release
Revision 1.0	Aug 13, 2025	Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0	Aug 13, 2025	Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0	Aug 13, 2025	Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0	Aug 13, 2025	Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Related structure data	38940MC M: map data used to model this data C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Assembly

Deposited unit

A: 50S ribosomal protein L31

B: 50S ribosomal protein L32

C: 50S ribosomal protein L33

D: 50S ribosomal protein L34

E: 50S ribosomal protein L35

F: 50S ribosomal protein L36

G: 30S ribosomal protein S2

H: 30S ribosomal protein S3

I: 30S ribosomal protein S4

J: 30S ribosomal protein S5

K: 30S ribosomal protein S6, fully modified isoform

L: 30S ribosomal protein S7

M: 30S ribosomal protein S8

N: 30S ribosomal protein S9

O: 30S ribosomal protein S10

P: 30S ribosomal protein S11

Q: 30S ribosomal protein S12

R: 30S ribosomal protein S13

S: 30S ribosomal protein S14

T: 30S ribosomal protein S15

U: 30S ribosomal protein S16

V: 30S ribosomal protein S17

W: 30S ribosomal protein S18

X: 30S ribosomal protein S19

Y: 30S ribosomal protein S20

Z: 30S ribosomal protein S21

b: 50S ribosomal protein L2

c: 50S ribosomal protein L3

d: 50S ribosomal protein L4

e: 50S ribosomal protein L5

f: 50S ribosomal protein L6

g: 50S ribosomal protein L9

i: 50S ribosomal protein L11

j: 50S ribosomal protein L13

k: 50S ribosomal protein L14

l: 50S ribosomal protein L15

m: 50S ribosomal protein L16

n: 50S ribosomal protein L17

o: 50S ribosomal protein L18

p: 50S ribosomal protein L19

q: 50S ribosomal protein L20

r: 50S ribosomal protein L21

s: 50S ribosomal protein L22

t: 50S ribosomal protein L23

u: 50S ribosomal protein L24

v: 50S ribosomal protein L25

w: 50S ribosomal protein L27

x: 50S ribosomal protein L28

y: 50S ribosomal protein L29

z: 50S ribosomal protein L30

1: 23S rRNA

2: 5S rRNA

3: 16S rRNA

4: mRNA

8: templete DNA strand

9: non-templete DNA strand

A1: DNA-directed RNA polymerase subunit alpha

A2: DNA-directed RNA polymerase subunit alpha

B1: DNA-directed RNA polymerase subunit beta'

B2: DNA-directed RNA polymerase subunit beta

W0: DNA-directed RNA polymerase subunit omega

NG: Transcription termination/antitermination protein NusG

5: tRNA(Phe)

6: tRNA(fMet)

a: Large ribosomal subunit protein uL1

0: Elongation factor G

h: Viomycin

hetero molecules

2.75 MDa, 67 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Idetical with deposited unit
defined by author
Evidence: electron microscopy, not applicable

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Components

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50S ribosomal protein ... , 30 types, 30 molecules ABCDEFbcdefgijklmnopqrstuvwxyz

#1: 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 K-12 (bacteria) / References: UniProt: P0A7M9
#2: Protein	50S ribosomal protein L32 / Large ribosomal subunit protein bL32 Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7N4
#3: Protein	50S ribosomal protein L33 / Large ribosomal subunit protein bL33 Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7N9
#4: Protein/peptide	50S ribosomal protein L34 / Large ribosomal subunit protein bL34 Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7P5
#5: 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 K-12 (bacteria) / References: UniProt: P0A7Q1
#6: 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 natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7Q6
#27: 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 K-12 (bacteria) / References: UniProt: P60422
#28: 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 K-12 (bacteria) / References: UniProt: P60438
#29: Protein	50S ribosomal protein L4 / Large ribosomal subunit protein uL4 Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P60723
#30: Protein	50S ribosomal protein L5 / Large ribosomal subunit protein uL5 Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P62399
#31: Protein	50S ribosomal protein L6 / Large ribosomal subunit protein uL6 Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG55
#32: Protein	50S ribosomal protein L9 / Large ribosomal subunit protein bL9 Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7R1
#33: 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 K-12 (bacteria) / References: UniProt: P0A7J7
#34: Protein	50S ribosomal protein L13 / Large ribosomal subunit protein uL13 Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AA10
#35: Protein	50S ribosomal protein L14 / Large ribosomal subunit protein uL14 Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0ADY3
#36: Protein	50S ribosomal protein L15 Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P02413
#37: 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 K-12 (bacteria) / References: UniProt: P0ADY7
#38: Protein	50S ribosomal protein L17 / Large ribosomal subunit protein bL17 Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG44
#39: Protein	50S ribosomal protein L18 / Large ribosomal subunit protein uL18 Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0C018
#40: Protein	50S ribosomal protein L19 / Large ribosomal subunit protein bL19 Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7K6
#41: Protein	50S ribosomal protein L20 / Large ribosomal subunit protein bL20 Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7L3
#42: Protein	50S ribosomal protein L21 / Large ribosomal subunit protein bL21 Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG48
#43: 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 K-12 (bacteria) / References: UniProt: P61175
#44: Protein	50S ribosomal protein L23 / Large ribosomal subunit protein uL23 Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0ADZ0
#45: Protein	50S ribosomal protein L24 / Large ribosomal subunit protein uL24 Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P60624
#46: Protein	50S ribosomal protein L25 / Large ribosomal subunit protein bL25 Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P68919
#47: 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 K-12 (bacteria) / References: UniProt: P0A7L8
#48: Protein	50S ribosomal protein L28 / Large ribosomal subunit protein bL28 Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7M2
#49: Protein	50S ribosomal protein L29 / Large ribosomal subunit protein uL29 Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7M6
#50: Protein	50S ribosomal protein L30 / Large ribosomal subunit protein uL30 Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG51

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

#7: Protein	30S ribosomal protein S2 / Small ribosomal subunit protein uS2 Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7V0
#8: Protein	30S ribosomal protein S3 / Small ribosomal subunit protein uS3 Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7V3
#9: Protein	30S ribosomal protein S4 / Small ribosomal subunit protein uS4 Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7V8
#10: Protein	30S ribosomal protein S5 / Small ribosomal subunit protein uS5 Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7W1
#11: Protein	30S ribosomal protein S6, fully modified isoform Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P02358
#12: Protein	30S ribosomal protein S7 / Small ribosomal subunit protein uS7 Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P02359
#13: Protein	30S ribosomal protein S8 / Small ribosomal subunit protein uS8 Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7W7
#14: Protein	30S ribosomal protein S9 / Small ribosomal subunit protein uS9 Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7X3
#15: 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 natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7R5
#16: Protein	30S ribosomal protein S11 / Small ribosomal subunit protein uS11 Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7R9
#17: Protein	30S ribosomal protein S12 / Small ribosomal subunit protein uS12 Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7S3
#18: Protein	30S ribosomal protein S13 / Small ribosomal subunit protein uS13 Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7S9
#19: Protein	30S ribosomal protein S14 / Small ribosomal subunit protein uS14 Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG59
#20: Protein	30S ribosomal protein S15 / Small ribosomal subunit protein uS15 Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0ADZ4
#21: Protein	30S ribosomal protein S16 / Small ribosomal subunit protein bS16 Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7T3
#22: Protein	30S ribosomal protein S17 / Small ribosomal subunit protein uS17 Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG63
#23: Protein	30S ribosomal protein S18 / Small ribosomal subunit protein bS18 Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7T7
#24: Protein	30S ribosomal protein S19 / Small ribosomal subunit protein uS19 Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7U3
#25: Protein	30S ribosomal protein S20 / Small ribosomal subunit protein bS20 Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7U7
#26: Protein	30S ribosomal protein S21 / Small ribosomal subunit protein bS21 Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P68679

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RNA chain , 6 types, 6 molecules 123456

#51: RNA chain	23S rRNA Mass: 941611.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 1929590828
#52: RNA chain	5S rRNA Mass: 38813.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: NR_103249
#53: RNA chain	16S rRNA Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 1789840096
#54: RNA chain	mRNA Mass: 8783.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#62: RNA chain	tRNA(Phe) Mass: 24485.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Plasmid: pBS -Phe / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 1845258627
#63: RNA chain	tRNA(fMet) Mass: 24802.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Plasmid: pBS-fMet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 1845258627

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DNA chain , 2 types, 2 molecules 89

#55: DNA chain	templete DNA strand Mass: 11230.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#56: DNA chain	non-templete DNA strand Mass: 11473.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules A1A2B1B2W0

#57: 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 / Plasmid: pVS10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#58: 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 K-12 (bacteria) / Gene: rpoC / Plasmid: pVS10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8T7, DNA-directed RNA polymerase
#59: 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 Plasmid: pVS10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8V2, DNA-directed RNA polymerase
#60: 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 / Plasmid: pVS10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A800, DNA-directed RNA polymerase

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Protein , 3 types, 3 molecules NGa0

#61: 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 K-12 (bacteria) / Gene: nusG, b3982, JW3945 / Plasmid: pIA247 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AFG0
#64: Protein	Large ribosomal subunit protein uL1 / 50S ribosomal protein L1 Mass: 24765.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7L0
#65: Protein	Elongation factor G / EF-G Mass: 79069.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fusA, far, fus, b3340, JW3302 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0A6M8, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

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Polypeptide(D) , 1 types, 1 molecules h

#66: Polypeptide(D)	Viomycin Type: Oligopeptide / Class: Antibiotic / Mass: 703.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Viomycin

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Non-polymers , 3 types, 3 molecules

#67: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#68: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#69: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄

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Details

Has ligand of interest	N
Has protein modification	Y

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Experimental details

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Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component	Name: Ternary complex of transcription-translation coupling complex Type: COMPLEX / Entity ID: #1-#66 / Source: MULTIPLE SOURCES
Molecular weight	Value: 3 MDa / Experimental value: NO
Source (natural)	Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)	Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solution	pH: 7.4
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Vitrification	Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment	Model: Talos Arctica / Image courtesy: FEI Company
Microscopy	Model: FEI TALOS ARCTICA
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recording	Electron dose: 47 e/Å² / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correction	Type: NONE
3D reconstruction	Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 626298 / Symmetry type: POINT

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50S ribosomal protein ... , 30 types, 30 molecules ABCDEFbcdefgijklmnopqrstuvwxyz

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

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RNA chain , 6 types, 6 molecules 123456

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DNA chain , 2 types, 2 molecules 89

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules A1A2B1B2W0

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Protein , 3 types, 3 molecules NGa0

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Polypeptide(D) , 1 types, 1 molecules h

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+50S ribosomal protein ... , 30 types, 30 molecules ABCDEFbcdefgijklmnopqrstuvwxyz

-30S ribosomal protein ... , 20 types, 20 molecules GHIJKLMNOPQRSTUVWXYZ

-RNA chain , 6 types, 6 molecules 123456

-DNA chain , 2 types, 2 molecules 89

-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules A1A2B1B2W0

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50S ribosomal protein ... , 30 types, 30 molecules ABCDEFbcdefgijklmnopqrstuvwxyz

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

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RNA chain , 6 types, 6 molecules 123456

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DNA chain , 2 types, 2 molecules 89

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules A1A2B1B2W0

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Protein , 3 types, 3 molecules NGa0

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Polypeptide(D) , 1 types, 1 molecules h

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Non-polymers , 3 types, 3 molecules

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Details

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Experimental details

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Experiment

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