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- PDB-6vz5: Escherichia coli transcription-translation complex D3 (TTC-D3) co... -

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Basic information

Entry
Database: PDB / ID: 6vz5
TitleEscherichia coli transcription-translation complex D3 (TTC-D3) containing mRNA with a 21 nt long spacer, NusG, and fMet-tRNAs at E-site and P-site
Components
  • (30S ribosomal protein ...) x 21
  • (50S ribosomal protein ...) x 29
  • (DNA-directed RNA polymerase subunit ...) x 4
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • E-site and P-site tRNA (fMet)
  • NT DNA
  • T DNA
  • Transcription termination/antitermination protein NusG
  • mRNA in the ribosomal RNA entrance pore
  • mRNA with 21 nt long spacer
KeywordsRIBOSOME / TRANSCRIPTION/TRANSLATION / bacterial coupled transcription-translation complex / TRANSCRIPTION-TRANSLATION complex
Function / homology
Function and homology information


DNA-templated transcription elongation / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / DNA-directed RNA polymerase complex / assembly of large subunit precursor of preribosome / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / transcription antitermination / regulation of cell growth ...DNA-templated transcription elongation / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / DNA-directed RNA polymerase complex / assembly of large subunit precursor of preribosome / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / mRNA 5'-UTR binding / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / large ribosomal subunit / ribosome binding / transferase activity / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / protein dimerization activity / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S1 / Ribosomal protein S1-like / RNA-binding domain, S1 / 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. ...Ribosomal protein S1 / Ribosomal protein S1-like / RNA-binding domain, S1 / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / S1 domain profile. / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / 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 S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / DNA-directed RNA polymerase, subunit beta-prime / Ribosomal protein L22, bacterial/chloroplast-type / RNA polymerase Rpb6 / Ribosomal protein L14P, bacterial-type
Similarity search - Domain/homology
: / : / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 ...: / : / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / DNA-directed RNA polymerase subunit alpha / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL17 / 30S ribosomal protein S1 / DNA-directed RNA polymerase subunit beta' / 30S ribosomal protein S7 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS16 / 50S ribosomal protein L23 / Large ribosomal subunit protein bL25 / 50S ribosomal protein L35 / 30S ribosomal protein S10 / 50S ribosomal protein L4 / 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 / 30S ribosomal protein S5 / 50S ribosomal protein L30 / 30S ribosomal protein S4 / 50S ribosomal protein L33 / 30S ribosomal protein S12 / 30S ribosomal protein S20 / 30S ribosomal protein S15 / 50S ribosomal protein L21 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L31 / 50S ribosomal protein L32 / 50S ribosomal protein L9 / 30S ribosomal protein S2 / 50S ribosomal protein L19 / 30S ribosomal protein S13 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS11 / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / 50S ribosomal protein L28 / Transcription termination/antitermination protein NusG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.9 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.
History
DepositionFeb 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 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
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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
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 beta'
AF: DNA-directed RNA polymerase subunit omega
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: mRNA in the ribosomal RNA entrance pore
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)2,694,06568
Polymers2,693,91065
Non-polymers1553
Water00
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 ... , 29 types, 29 molecules 01234bcefghijklmnopqrstuvwxyz

#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
#39: 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
#40: 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
#42: 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
#43: 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
#44: 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
#45: 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
#46: 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
#47: 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
#48: 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
#49: 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
#50: 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
#51: 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
#52: 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
#53: 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
#54: 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
#55: 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
#56: 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
#57: 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
#58: 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
#59: 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
#60: 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, EAXG_02993 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3LC97
#61: 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
#62: 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
#63: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MAS6

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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: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Production host: synthetic construct (others)
#7: DNA chain T DNA


Mass: 10956.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Production host: synthetic construct (others)

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RNA chain , 6 types, 7 molecules 7ABDYad

#8: RNA chain mRNA with 21 nt long spacer


Mass: 11993.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Production host: synthetic construct (others)
#9: 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)
#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
#37: RNA chain mRNA in the ribosomal RNA entrance pore


Mass: 873.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Production host: synthetic construct (others)
#38: RNA chain 23S rRNA


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
#41: RNA chain 5S rRNA


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 ... , 4 types, 5 molecules AAACADAEAF

#10: 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) / Strain: MRE600 / Gene: rpoB, Z5560, ECs4910 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8V4, 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) / Strain: MRE600 / Gene: rpoA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A073G207, 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) / Strain: MRE600 / Gene: rpoC, BvCmsKKP036_03580 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A4S1NBU2, 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) / Strain: MRE600 / Gene: rpoZ, Z5075, ECs4524 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A802, DNA-directed RNA polymerase

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Protein , 1 types, 1 molecules AB

#11: 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, V415_18420 / Production host: Escherichia coli (E. coli) / References: UniProt: V8K3D7

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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 / Gene: EAXG_00304 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3LHG1
#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 / Small ribosomal subunit protein uS11


Mass: 12487.200 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsK, b3297, JW3259 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R9
#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

#64: Chemical ChemComp-MG / MAGNESIUM ION


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


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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Escherichia coli transcription-translation complex D3 (TTC-D3) containing mRNA with a 21 nt long spacer, NusG, and fMet-tRNAs at E-site and P-site
Type: COMPLEX / Entity ID: #1-#63 / 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

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6440 / Symmetry type: POINT

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