[English] 日本語
Yorodumi
- PDB-6vz3: Escherichia coli transcription-translation complex D2 (TTC-D2) co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vz3
TitleEscherichia coli transcription-translation complex D2 (TTC-D2) containing mRNA with a 27 nt long spacer
Components
  • (30S ribosomal protein ...) x 21
  • (50S ribosomal protein ...) x 29
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • E-site tRNA (fMet)
  • NT DNA
  • T DNA
  • Transcription termination/antitermination protein NusG
  • mRNA in the ribosomal RNA entrance poreMessenger RNA
  • mRNA with 27 nt long spacer
KeywordsRIBOSOME / TRANSCRIPTION/TRANSLATION / bacterial coupled transcription-translation complex / TRANSCRIPTION-TRANSLATION complex
Function / homology
Function and homology information


DNA-templated transcription elongation / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribonucleoside binding ...DNA-templated transcription elongation / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytosolic small ribosomal subunit / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / rRNA binding / protein dimerization activity / 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. / NusG-like / Transcription termination factor nusG / RNA-binding domain, S1 / NusG, N-terminal ...: / Ribosomal protein S1 / Ribosomal protein S1-like / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / NusG-like / Transcription termination factor nusG / RNA-binding domain, S1 / 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 / Ribosomal protein L25, short-form / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / Ribosomal protein L31 type A / S1 RNA binding domain / Ribosomal protein S21 superfamily / Ribosomal protein S21 / S1 domain / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein 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 L17 signature. / 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 L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / 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 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 L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / RNA polymerase Rpb6 / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type
Similarity search - Domain/homology
: / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / 30S ribosomal protein S10 ...: / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / 30S ribosomal protein S10 / 50S ribosomal protein L29 / 50S ribosomal protein L27 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein bL36 / 30S ribosomal protein S18 / Large ribosomal subunit protein bL17 / 30S ribosomal protein S3 / Small ribosomal subunit protein bS6 / 30S ribosomal protein S1 / 30S ribosomal protein S13 / Large ribosomal subunit protein bL19 / Transcription termination/antitermination protein NusG / 50S ribosomal protein L6 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta' / 30S ribosomal protein S1 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS2 / 50S ribosomal protein L23 / 30S ribosomal protein S20 / Large ribosomal subunit protein bL25 / 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 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / 50S ribosomal protein L35 / Small ribosomal subunit protein uS12 / 30S ribosomal protein S14 / 50S ribosomal protein L30 / 50S ribosomal protein L28 / 50S ribosomal protein L20 / 30S ribosomal protein S4 / 50S ribosomal protein L33 / Small ribosomal subunit protein uS11 / DNA-directed RNA polymerase subunit beta / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / 30S ribosomal protein S7 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL5 / DNA-directed RNA polymerase subunit omega / 30S ribosomal protein S9 / Large ribosomal subunit protein bL31
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-21483
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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 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 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)2,602,57368
Polymers2,602,41865
Non-polymers1553
Water0
1


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

-
Components

+
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) / 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) / 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) / 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) / 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) / 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 (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A069XRX8
#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 (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: J7RMJ2
#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) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A069XF36
#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) / Production host: Escherichia coli (E. coli) / References: UniProt: I2X1N4
#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) / Production host: Escherichia coli (E. coli) / References: UniProt: V0YYV3
#45: Protein 50S ribosomal protein L2 /


Mass: 29663.244 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: 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) / Production host: Escherichia coli (E. coli) / References: UniProt: E3PJQ3
#47: Protein 50S ribosomal protein L3 /


Mass: 22277.535 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: 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) / Production host: Escherichia coli (E. coli) / References: UniProt: L4IX08
#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) / 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) / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: S1EUW9
#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) / Production host: Escherichia coli (E. coli) / References: UniProt: G0F552
#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) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B7PA13
#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) / 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) / 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) / 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) / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A037Y8L6
#59: Protein 50S ribosomal protein L16 /


Mass: 15312.269 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: 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) / 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 (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: F4TL27
#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 (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P8C2I6
#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) / Production host: Escherichia coli (E. coli) / References: UniProt: L3CCT0

-
DNA chain , 2 types, 2 molecules 56

#6: DNA chain NT DNA


Mass: 12359.141 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)

-
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 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: 1126835761
#16: RNA chain 16S rRNA /


Mass: 497240.844 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)
#37: RNA chain mRNA in the ribosomal RNA entrance pore / Messenger RNA


Mass: 873.540 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)
#38: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 941269.250 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 / 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) / Production host: Escherichia coli (E. coli) / References: GenBank: 1273279017

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

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


Mass: 150820.875 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: P0A8V4, DNA-directed RNA polymerase
#12: Protein DNA-directed RNA polymerase subunit alpha / Polymerase


Mass: 25497.023 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: UniProt: A0A5F0PYH4, DNA-directed RNA polymerase
#13: Protein DNA-directed RNA polymerase subunit beta / Polymerase


Mass: 150436.344 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: A0A659GYB8, DNA-directed RNA polymerase
#14: Protein DNA-directed RNA polymerase subunit omega / Polymerase


Mass: 9362.485 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: T9C803, DNA-directed RNA polymerase

-
Protein , 1 types, 1 molecules AB

#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) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V3VM65

+
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) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A222QU44
#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) / 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) / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: C3TPN2
#20: Protein 30S ribosomal protein S1 /


Mass: 38487.602 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: A0A3Z9BLB3, UniProt: A0A7H4YPL5*PLUS
#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) / 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) / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: F4TL26
#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) / 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) / 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) / 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) / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A069XEJ0
#29: Protein 30S ribosomal protein S11 /


Mass: 12487.200 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: P0A7R9
#30: Protein 30S ribosomal protein S12 /


Mass: 13683.053 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: I2UHF1
#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) / Production host: Escherichia coli (E. coli) / References: UniProt: I2X0X3
#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) / 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) / 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) / 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) / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P8BX31

-
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

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Escherichia coli transcription-translation complex D2 (TTC-D2) containing mRNA with a 27 nt long spacer, NusG, and fMet-tRNAs at E-site and P-site
Type: COMPLEX / Entity ID: #1-#7, #9, #11-#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 FIELDBright-field microscopy
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: 6237 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more