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- PDB-6vys: Escherichia coli transcription-translation complex A1 (TTC-A1) co... -

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Entry
Database: PDB / ID: 6vys
TitleEscherichia coli transcription-translation complex A1 (TTC-A1) containing a 21 nt long mRNA spacer, NusG, and fMet-tRNAs at E-site and P-site
Components
  • (30S ribosomal protein ...) x 21
  • (50S ribosomal protein ...) x 32
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 2
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • DNA-directed RNA polymerase subunitPolymerase
  • E-site and P-site tRNA (fMet)
  • NT DNA
  • T DNA
  • Transcription termination/antitermination protein NusG
  • mRNA with 21 nt long spacer
KeywordsRIBOSOME / TRANSCRIPTION/TRANSLATION / Bacterial transcription-translation complex / TRANSCRIPTION / TRANSCRIPTION-TRANSLATION complex
Function / homology
Function and homology information


DNA-templated transcription, elongation / regulation of DNA-templated transcription, elongation / positive regulation of ribosome biogenesis / transcription antitermination / mature ribosome assembly / assembly of large subunit precursor of preribosome / DNA-templated transcription, termination / ribonucleoside binding / regulation of cell growth / DNA-directed 5'-3' RNA polymerase activity ...DNA-templated transcription, elongation / regulation of DNA-templated transcription, elongation / positive regulation of ribosome biogenesis / transcription antitermination / mature ribosome assembly / assembly of large subunit precursor of preribosome / DNA-templated transcription, termination / ribonucleoside binding / regulation of cell growth / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / ribosome binding / 5S rRNA binding / ribosome biogenesis / cytosolic small ribosomal subunit / small ribosomal subunit / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / transcription, DNA-templated / protein dimerization activity / mRNA binding / magnesium ion binding / RNA binding / DNA binding / zinc ion binding / metal ion binding / cytosol
Ribosomal protein L27, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L10e/L16 / Ribosomal protein L30, conserved site / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L19, conserved site ...Ribosomal protein L27, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L10e/L16 / Ribosomal protein L30, conserved site / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L33, conserved site / Ribosomal protein S10, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S3, conserved site / DNA-directed RNA polymerase, beta subunit, external 1 domain / Ribosomal protein L6, bacterial-type / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein S11, bacterial-type / Ribosomal protein L30, ferredoxin-like fold domain / Transcription antitermination protein, NusG, bacteria, conserved site / Ribosomal protein L6, alpha-beta domain / DNA-directed RNA polymerase, alpha subunit / Ribosomal protein L7/L12, oligomerisation / Translation protein SH3-like domain superfamily / Translation protein, beta-barrel domain superfamily / K homology domain superfamily, prokaryotic type / Ribosomal protein L9/RNase H1, N-terminal / S15/NS1, RNA-binding / DNA-directed RNA polymerase beta subunit, bacterial-type / Ribosomal protein S13-like, H2TH / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / RNA polymerase, alpha subunit, C-terminal / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase, subunit 2 / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / 50S ribosomal protein uL4 / Ribosomal protein L25/L23 / Ribosomal protein S5, N-terminal / Ribosomal protein L7/L12, C-terminal / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / RNA polymerase Rpb2, OB-fold / Ribosomal protein L2, domain 3 / 30S ribosomal protein S17 / Ribosomal protein L25, short-form / RNA polymerase, beta subunit, protrusion / Ribosomal protein S1-like / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / Ribosomal protein L28/L24 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein L31 type A / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein S19/S15, superfamily / Ribosomal protein L36 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S20 superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L5, conserved site / Ribosomal protein L9, C-terminal / Ribosomal protein L9, N-terminal / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site
30S ribosomal protein S9 / 50S ribosomal protein L9 / 50S ribosomal protein L32 / 50S ribosomal protein L31 / 50S ribosomal protein L13 / 50S ribosomal protein L10 / 50S ribosomal protein L21 / 30S ribosomal protein S15 / 30S ribosomal protein S20 / 30S ribosomal protein S12 ...30S ribosomal protein S9 / 50S ribosomal protein L9 / 50S ribosomal protein L32 / 50S ribosomal protein L31 / 50S ribosomal protein L13 / 50S ribosomal protein L10 / 50S ribosomal protein L21 / 30S ribosomal protein S15 / 30S ribosomal protein S20 / 30S ribosomal protein S12 / 50S ribosomal protein L11 / 50S ribosomal protein L19 / 30S ribosomal protein S2 / gb:1732209707: / 30S ribosomal protein S13 / 50S ribosomal protein L20 / 30S ribosomal protein S6 / 50S ribosomal protein L27 / DNA-directed RNA polymerase subunit beta / 50S ribosomal protein L16 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L28 / Transcription termination/antitermination protein NusG / 50S ribosomal protein L7/L12 / gb:1384458579: / 30S ribosomal protein S4 / gb:937521852: / 50S ribosomal protein L33 / 50S ribosomal protein L4 / 50S ribosomal protein L30 / 50S ribosomal protein L23 / 50S ribosomal protein L15 / DNA-directed RNA polymerase subunit alpha / 30S ribosomal protein S18 / 50S ribosomal protein L36 / 30S ribosomal protein S21 / 30S ribosomal protein S7 / DNA-directed RNA polymerase subunit beta' / 30S ribosomal protein S11 / 30S ribosomal protein S3 / 50S ribosomal protein L34 / 30S ribosomal protein S16 / 30S ribosomal protein S1 / 50S ribosomal protein L17 / 50S ribosomal protein L25 / 30S ribosomal protein S5 / 50S ribosomal protein L35 / 30S ribosomal protein S10 / 30S ribosomal protein S19 / 50S ribosomal protein L22 / 50S ribosomal protein L29 / 30S ribosomal protein S17 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L5 / 30S ribosomal protein S14 / 30S ribosomal protein S8 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / gb:1273279017:
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMolodtsov, V. / Wang, C. / Su, M. / Ebright, R.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Science / Year: 2020
Title: Structural basis of transcription-translation coupling.
Authors: Chengyuan Wang / Vadim Molodtsov / Emre Firlar / Jason T Kaelber / Gregor Blaha / Min Su / Richard H Ebright /
Abstract: In bacteria, transcription and translation are coupled processes in which the movement of RNA polymerase (RNAP)-synthesizing messenger RNA (mRNA) is coordinated with the movement of the first ...In bacteria, transcription and translation are coupled processes in which the movement of RNA polymerase (RNAP)-synthesizing messenger RNA (mRNA) is coordinated with the movement of the first ribosome-translating mRNA. Coupling is modulated by the transcription factors NusG (which is thought to bridge RNAP and the ribosome) and NusA. Here, we report cryo-electron microscopy structures of transcription-translation complexes (TTCs) containing different-length mRNA spacers between RNAP and the ribosome active-center P site. Structures of TTCs containing short spacers show a state incompatible with NusG bridging and NusA binding (TTC-A, previously termed "expressome"). Structures of TTCs containing longer spacers reveal a new state compatible with NusG bridging and NusA binding (TTC-B) and reveal how NusG bridges and NusA binds. We propose that TTC-B mediates NusG- and NusA-dependent transcription-translation coupling.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
0: 50S ribosomal protein L21
1: 50S ribosomal protein L22
2: 50S ribosomal protein L23
3: 50S ribosomal protein L24
4: 50S ribosomal protein L25
5: NT DNA
6: T DNA
7: mRNA with 21 nt long spacer
9: 50S ribosomal protein L10
A: E-site and P-site tRNA (fMet)
AA: DNA-directed RNA polymerase subunit beta
AB: Transcription termination/antitermination protein NusG
AC: DNA-directed RNA polymerase subunit alpha
AD: DNA-directed RNA polymerase subunit alpha
AE: DNA-directed RNA polymerase subunit
B: E-site and P-site tRNA (fMet)
C: 30S ribosomal protein S18
D: 16S rRNA
E: 30S ribosomal protein S20
F: 30S ribosomal protein S21
G: 30S ribosomal protein S2
H: 30S ribosomal protein S1
I: 30S ribosomal protein S3
J: 30S ribosomal protein S4
K: 30S ribosomal protein S5
L: 30S ribosomal protein S6
M: 30S ribosomal protein S7
N: 30S ribosomal protein S8
O: 30S ribosomal protein S9
P: 30S ribosomal protein S10
Q: 30S ribosomal protein S11
R: 30S ribosomal protein S12
S: 30S ribosomal protein S14
T: 30S ribosomal protein S15
U: 30S ribosomal protein S16
V: 30S ribosomal protein S17
W: 30S ribosomal protein S19
X: 30S ribosomal protein S13
Y: 50S ribosomal protein L11
Z: 50S ribosomal protein L7/L12
a: 23S rRNA
b: 50S ribosomal protein L27
c: 50S ribosomal protein L28
d: 5S rRNA
e: 50S ribosomal protein L29
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: 50S ribosomal protein L4
m: 50S ribosomal protein L34
n: 50S ribosomal protein L5
o: 50S ribosomal protein L35
p: 50S ribosomal protein L6
q: 50S ribosomal protein L36
r: 50S ribosomal protein L9
s: 50S ribosomal protein L13
t: 50S ribosomal protein L14
u: 50S ribosomal protein L15
v: 50S ribosomal protein L16
w: 50S ribosomal protein L17
x: 50S ribosomal protein L18
y: 50S ribosomal protein L19
z: 50S ribosomal protein L20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,724,02969
Polymers2,723,87466
Non-polymers1553
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 32 types, 32 molecules 012349YZbcefghijklmnopqrstuvwxyz

#1: Protein 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplU / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZEN7
#2: Protein 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplV / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G0
#3: Protein 50S ribosomal protein L23 /


Mass: 11222.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplW / Production host: Escherichia coli (E. coli) / References: UniProt: D7X2Z9
#4: Protein 50S ribosomal protein L24 /


Mass: 11339.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplX / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G6
#5: Protein 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplY / Production host: Escherichia coli (E. coli) / References: UniProt: D7XH79
#9: Protein 50S ribosomal protein L10 /


Mass: 17736.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplJ / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZA73
#37: Protein 50S ribosomal protein L11 /


Mass: 14894.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplK / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZA71
#38: Protein 50S ribosomal protein L7/L12 / Ribosome


Mass: 12309.155 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplL / Production host: Escherichia coli (E. coli) / References: UniProt: V0AEG5
#40: Protein 50S ribosomal protein L27 / / Large ribosomal subunit protein bL27


Mass: 9146.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpmA, b3185, JW3152 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L8
#41: Protein 50S ribosomal protein L28 /


Mass: 9027.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpmB / Production host: Escherichia coli (E. coli) / References: UniProt: S0YB49
#43: Protein 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpmC / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G3
#44: Protein 50S ribosomal protein L30 /


Mass: 6554.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpmD / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9H3
#45: Protein 50S ribosomal protein L31 /


Mass: 7887.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpmE / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZFP6
#46: Protein 50S ribosomal protein L2 / / Large ribosomal subunit protein uL2


Mass: 29923.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplB, b3317, JW3279 / Production host: Escherichia coli (E. coli) / References: UniProt: P60422
#47: Protein 50S ribosomal protein L32 /


Mass: 6463.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpmF / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZGG2
#48: Protein 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplC, b3320, JW3282 / Production host: Escherichia coli (E. coli) / References: UniProt: P60438
#49: Protein 50S ribosomal protein L33 /


Mass: 6388.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpmG / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9P0
#50: Protein 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplD / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9F6
#51: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpmH / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGC4
#52: Protein 50S ribosomal protein L5 /


Mass: 20333.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplE / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G7
#53: Protein 50S ribosomal protein L35 /


Mass: 7313.032 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpmI / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z814
#54: Protein 50S ribosomal protein L6 /


Mass: 18932.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplF / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9H0
#55: Protein/peptide 50S ribosomal protein L36 /


Mass: 4377.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpmJ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2L017
#56: Protein 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplI / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZI15
#57: Protein 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplM / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZET0
#58: Protein 50S ribosomal protein L14 /


Mass: 13565.067 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplN / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G5
#59: Protein 50S ribosomal protein L15 /


Mass: 15008.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplO / Production host: Escherichia coli (E. coli) / References: UniProt: A0A037Y8L6
#60: Protein 50S ribosomal protein L16 / / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplP, b3313, JW3275 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY7
#61: Protein 50S ribosomal protein L17 /


Mass: 14393.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplQ, ECCG_03701 / Production host: Escherichia coli (E. coli) / References: UniProt: D6I1Y5
#62: Protein 50S ribosomal protein L18 /


Mass: 12794.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplR / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9H1
#63: Protein 50S ribosomal protein L19 /


Mass: 13159.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplS / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZKU3
#64: Protein 50S ribosomal protein L20 /


Mass: 13528.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplT, A13W_00675 / Production host: Escherichia coli (E. coli) / References: UniProt: L3CCT0

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DNA chain , 2 types, 2 molecules 56

#6: DNA chain NT DNA


Mass: 11042.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain T DNA


Mass: 10956.012 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 21 nt long spacer


Mass: 11687.655 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: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Production host: Escherichia coli (E. coli) / References: GenBank: 1384458579
#16: RNA chain 16S rRNA


Mass: 499690.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Production host: Escherichia coli (E. coli) / References: GenBank: 1732209707
#39: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 941635.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Production host: Escherichia coli (E. coli) / References: GenBank: 937521852
#42: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38790.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Production host: Escherichia coli (E. coli) / References: GenBank: 1273279017

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DNA-directed RNA polymerase subunit ... , 2 types, 3 molecules AAACAD

#11: Protein DNA-directed RNA polymerase subunit beta / Polymerase / 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) / Strain: MRE600 / Gene: rpoB, Z5560, ECs4910 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8V4, DNA-directed RNA polymerase
#13: Protein DNA-directed RNA polymerase subunit alpha / Polymerase / 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) / Strain: MRE600 / Gene: rpoA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A073G207, DNA-directed RNA polymerase

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Protein , 2 types, 2 molecules ABAE

#12: 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) / Strain: MRE600 / Gene: nusG / Production host: Escherichia coli (E. coli) / References: UniProt: U9XYQ6
#14: Protein DNA-directed RNA polymerase subunit / Polymerase


Mass: 150436.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpoC, ELV15_17980 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A659GYB8, DNA-directed RNA polymerase

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30S ribosomal protein ... , 21 types, 21 molecules CEFGHIJKLMNOPQRSTUVWX

#15: Protein 30S ribosomal protein S18 /


Mass: 9005.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2KXL3
#17: Protein 30S ribosomal protein S20 /


Mass: 9708.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsT / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZAS2
#18: Protein 30S ribosomal protein S21 /


Mass: 8524.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsU / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2L2J1
#19: Protein 30S ribosomal protein S2 /


Mass: 26781.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsB / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZK99
#20: Protein 30S ribosomal protein S1 /


Mass: 61238.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Production host: Escherichia coli (E. coli) / References: UniProt: D6HUW2
#21: Protein 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsC / Production host: Escherichia coli (E. coli) / References: UniProt: B7MCS9
#22: Protein 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 (E. coli) / Strain: MRE600 / Gene: rpsD / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9H7
#23: Protein 30S ribosomal protein S5 /


Mass: 17629.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsE / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9H2
#24: Protein 30S ribosomal protein S6 / / Small ribosomal subunit protein bS6


Mass: 15727.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsF, b4200, JW4158 / Production host: Escherichia coli (E. coli) / References: UniProt: P02358
#25: Protein 30S ribosomal protein S7 /


Mass: 20055.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsG, GHR40_06850 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5Q2GFB5
#26: Protein 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsH / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G9
#27: Protein 30S ribosomal protein S9 /


Mass: 14886.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsI / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZES9
#28: Protein 30S ribosomal protein S10 /


Mass: 11755.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsJ / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9F4
#29: Protein 30S ribosomal protein S11 /


Mass: 13870.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsK / Production host: Escherichia coli (E. coli) / References: UniProt: B7MCR3
#30: Protein 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsL / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZAN0
#31: Protein 30S ribosomal protein S14 /


Mass: 11606.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsN / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G8
#32: Protein 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 (E. coli) / Strain: MRE600 / Gene: rpsO / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZEL4
#33: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsP / Production host: Escherichia coli (E. coli) / References: UniProt: B7MIU7
#34: Protein 30S ribosomal protein S17 /


Mass: 9724.491 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsQ / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G4
#35: Protein 30S ribosomal protein S19 /


Mass: 10455.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsS / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9F9
#36: Protein 30S ribosomal protein S13 /


Mass: 13128.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsM / Production host: Escherichia coli (E. coli) / References: UniProt: H4UQ02

+
Non-polymers , 2 types, 3 molecules

#65: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#66: Chemical ChemComp-ZN / ZINC ION / Zinc


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

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Details

Has ligand of interestN

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Experimental details

-
Experiment

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

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Sample preparation

ComponentName: Escherichia coli transcription-translation complex A1 (TTC-A1) containing a 21 nt long mRNA spacer, NusG, and fMet-tRNAs at E-site and P-site
Type: COMPLEX / Entity ID: #1-#64 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29704 / Symmetry type: POINT

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