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- PDB-6vz7: Escherichia coli transcription-translation complex C1 (TTC-C1) co... -

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Basic information

Entry
Database: PDB / ID: 6vz7
TitleEscherichia coli transcription-translation complex C1 (TTC-C1) containing a 27 nt long mRNA spacer, NusG, and fMet-tRNAs at P-site and E-site
Components
  • (30S ribosomal protein ...) x 21
  • (50S ribosomal protein ...) x 29
  • (DNA-directed RNA polymerase subunit ...) x 3
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • DNA-directed RNA polymerase subunit
  • 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 27 nt long spacer
KeywordsRIBOSOME / Bacterial transcription-translation coupled complex / TRANSCRIPTION
Function / homology
Function and homology information


DNA-templated transcription elongation / DnaA-L2 complex / DNA-directed RNA polymerase complex / negative regulation of DNA-templated DNA replication initiation / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...DNA-templated transcription elongation / DnaA-L2 complex / DNA-directed RNA polymerase complex / negative regulation of DNA-templated DNA replication initiation / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / small ribosomal subunit rRNA binding / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / protein dimerization activity / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S1 / Ribosomal protein S1-like / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / RNA-binding domain, S1 / 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 / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / RNA-binding domain, S1 / 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 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Ribosomal protein 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 / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / S1 domain / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / 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 L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type / RNA polymerase Rpb6 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, plastid/chloroplast / RNA polymerase, subunit omega/Rpo6/RPB6
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 / 50S ribosomal protein L19 / 50S ribosomal protein L30 / 30S ribosomal protein S14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein bL35 / DNA-directed RNA polymerase subunit beta / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / DNA-directed RNA polymerase subunit omega / Large ribosomal subunit protein bL17 / 30S ribosomal protein S3 / Small ribosomal subunit protein bS6 / Transcription termination/antitermination protein NusG / 50S ribosomal protein L28 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta' / 30S ribosomal protein S18 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS2 / 30S ribosomal protein S1 / 50S ribosomal protein L23 / 30S ribosomal protein S20 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS15 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L14 / 50S ribosomal protein L21 / 50S ribosomal protein L13 / 50S ribosomal protein L9 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein bS21 / 50S ribosomal protein L6 / 30S ribosomal protein S5 / 50S ribosomal protein L18 / 50S ribosomal protein L27 / 30S ribosomal protein S10 / 50S ribosomal protein L29 / 30S ribosomal protein S4 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / 30S ribosomal protein S7 / Small ribosomal subunit protein uS19 / 50S ribosomal protein L5 / 30S ribosomal protein S9 / Large ribosomal subunit protein bL31 / 50S ribosomal protein L20 / 50S ribosomal protein L33 / 30S ribosomal protein S12
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 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.
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 16, 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 27 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
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)2,623,77668
Polymers2,623,62165
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) / 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) / Gene: rplV / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G0
#3: Protein 50S ribosomal protein L23


Mass: 10661.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplW / Production host: Escherichia coli (E. coli) / References: UniProt: D6I208
#4: Protein 50S ribosomal protein L24


Mass: 11208.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplX / Production host: Escherichia coli (E. coli) / References: UniProt: D7XKZ6
#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) / Gene: rplY / Production host: Escherichia coli (E. coli) / References: UniProt: D7XH79
#39: Protein 50S ribosomal protein L27


Mass: 8275.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli / Gene: rpmA / Production host: Escherichia coli (E. coli) / References: UniProt: I2X5R7
#40: Protein 50S ribosomal protein L28


Mass: 8896.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli / Gene: rpmB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A556Y8P1
#42: Protein 50S ribosomal protein L29


Mass: 7155.267 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmC / Production host: Escherichia coli (E. coli) / References: UniProt: I2X6R6
#43: Protein 50S ribosomal protein L30


Mass: 6423.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A073FR56
#44: Protein 50S ribosomal protein L31


Mass: 7516.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmE / Production host: Escherichia coli (E. coli) / References: UniProt: V0YYV3
#45: Protein 50S ribosomal protein L2 / Large ribosomal subunit protein uL2


Mass: 29663.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplB / Production host: Escherichia coli (E. coli) / References: UniProt: P60422
#46: Protein 50S ribosomal protein L32


Mass: 6332.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmF / Production host: Escherichia coli (E. coli) / References: UniProt: D7XI28
#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) / Gene: rplC / Production host: Escherichia coli (E. coli) / References: UniProt: P60438
#48: Protein 50S ribosomal protein L33


Mass: 6057.179 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmG / Production host: Escherichia coli (E. coli) / References: UniProt: V6FW62
#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) / 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) / Gene: rpmH / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGC4
#51: Protein 50S ribosomal protein L5


Mass: 20073.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplE / Production host: Escherichia coli (E. coli) / References: UniProt: T6LFZ6
#52: Protein 50S ribosomal protein L35


Mass: 7181.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A0FFH2
#53: Protein 50S ribosomal protein L6


Mass: 18672.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplF / Production host: Escherichia coli (E. coli) / References: UniProt: E9YV47
#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) / 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) / 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) / 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) / Gene: rplP / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY7
#60: Protein 50S ribosomal protein L17


Mass: 13592.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplQ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2T1LEK9
#61: Protein 50S ribosomal protein L18


Mass: 12663.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli / Gene: rplR / Production host: Escherichia coli (E. coli) / References: UniProt: H4JDL8
#62: Protein 50S ribosomal protein L19


Mass: 13028.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli / Gene: rplS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A069XKC0
#63: Protein 50S ribosomal protein L20


Mass: 13396.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplT / Production host: Escherichia coli (E. coli) / References: UniProt: V6FS92

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DNA chain , 2 types, 2 molecules 56

#6: DNA chain NT DNA


Mass: 8281.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain T DNA


Mass: 8155.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain , 6 types, 7 molecules 7ABDYad

#8: RNA chain mRNA with 27 nt long spacer


Mass: 5196.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) 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) / Production host: Escherichia coli (E. coli) / References: GenBank: 1848954948
#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) / 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: obtained synthetically / Source: (synth.) synthetic construct (others)
#38: RNA chain 23S rRNA


Mass: 941526.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#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) / Production host: Escherichia coli (E. coli) / References: GenBank: 1273279017

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DNA-directed RNA polymerase subunit ... , 3 types, 4 molecules AAACADAF

#10: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150689.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoB / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0A0GWV9, DNA-directed RNA polymerase
#12: Protein DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 25497.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A5F0PYH4, DNA-directed RNA polymerase
#14: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 9362.485 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1X3IVJ5, DNA-directed RNA polymerase

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Protein , 2 types, 2 molecules ABAE

#11: Protein Transcription termination/antitermination protein NusG


Mass: 12925.917 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nusG / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V3VM65
#13: Protein DNA-directed RNA polymerase subunit


Mass: 150436.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC / 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: 7734.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6D2XHZ3
#17: Protein 30S ribosomal protein S20


Mass: 9577.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsT / Production host: Escherichia coli (E. coli) / References: UniProt: D7X3A7
#18: Protein 30S ribosomal protein S21


Mass: 8392.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsU / Production host: Escherichia coli (E. coli) / References: UniProt: E9TH65
#19: Protein 30S ribosomal protein S2


Mass: 25072.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsB / Production host: Escherichia coli (E. coli) / References: UniProt: C3TPN2
#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) / Production host: Escherichia coli (E. coli) / References: UniProt: D6HUW2
#21: Protein 30S ribosomal protein S3


Mass: 23248.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A376HTV6
#22: Protein 30S ribosomal protein S4


Mass: 23383.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsD / Production host: Escherichia coli (E. coli) / References: UniProt: L3PZ69
#23: Protein 30S ribosomal protein S5


Mass: 16475.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsE / Production host: Escherichia coli (E. coli) / References: UniProt: F4SQ30
#24: Protein 30S ribosomal protein S6


Mass: 12125.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsF / Production host: Escherichia coli (E. coli) / References: UniProt: A0A376ZL25
#25: Protein 30S ribosomal protein S7


Mass: 16861.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsG / Production host: Escherichia coli (E. coli) / References: UniProt: S1D5F0
#26: Protein 30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsH / Production host: Escherichia coli (E. coli) / References: UniProt: D8A1L7
#27: Protein 30S ribosomal protein S9


Mass: 14554.882 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsI / Production host: Escherichia coli (E. coli) / References: UniProt: T9TH92
#28: Protein 30S ribosomal protein S10


Mass: 11254.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsJ / Production host: Escherichia coli (E. coli) / References: UniProt: I2X6I5
#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) / Gene: rpsK / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R9
#30: Protein 30S ribosomal protein S12


Mass: 13636.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsL / Production host: Escherichia coli (E. coli) / References: UniProt: V6FZ95
#31: Protein 30S ribosomal protein S14


Mass: 11475.364 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsN / Production host: Escherichia coli (E. coli) / References: UniProt: A0A073G231
#32: Protein 30S ribosomal protein S15


Mass: 10159.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsO / Production host: Escherichia coli (E. coli) / References: UniProt: D7XN21
#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) / Gene: rpsP / Production host: Escherichia coli (E. coli) / References: UniProt: B7MIU7
#34: Protein 30S ribosomal protein S17


Mass: 9263.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsQ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A080IK26
#35: Protein 30S ribosomal protein S19


Mass: 9421.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsS / Production host: Escherichia coli (E. coli) / References: UniProt: S1EA57
#36: Protein 30S ribosomal protein S13


Mass: 12868.091 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsM / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3ML81

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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

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Escherichia coli transcription-translation complex C1 (TTC-C1) containing a 27 nt long mRNA spacer, NusG, and fMet-tRNAs at P-site and E-site
Type: COMPLEX / Entity ID: #1-#63 / Source: RECOMBINANT
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
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: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5979 / Symmetry type: POINT

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