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- PDB-6ztj: E. coli 70S-RNAP expressome complex in NusG-coupled state (38 nt ... -

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Basic information

Entry
Database: PDB / ID: 6ztj
TitleE. coli 70S-RNAP expressome complex in NusG-coupled state (38 nt intervening mRNA)
Components
  • (30S ribosomal protein ...) x 21
  • (50S ribosomal protein ...) x 31
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Non-template DNA strand
  • Phe-NH-tRNA(Phe) A-site
  • Template DNA strand
  • Transcription termination/antitermination protein NusG
  • mRNAMessenger RNA
  • tRNA(fmet) P-site
KeywordsGENE REGULATION / Transcription / Translation / Expressome / Ribosome / RNA polymerase
Function / homology
Function and homology information


negative regulation of cytoplasmic translation / DNA-templated transcription, elongation / regulation of DNA-templated transcription, elongation / RNA polymerase complex / stringent response / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / transcription antitermination / translation repressor activity ...negative regulation of cytoplasmic translation / DNA-templated transcription, elongation / regulation of DNA-templated transcription, elongation / RNA polymerase complex / stringent response / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / transcription antitermination / translation repressor activity / mature ribosome assembly / translational termination / ribosome assembly / ribonucleoside binding / translation repressor activity, mRNA regulatory element binding / polysomal ribosome / DNA-templated transcription, termination / assembly of large subunit precursor of preribosome / regulation of cell growth / response to reactive oxygen species / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / cytoplasmic translation / ribosome biogenesis / cytosolic large ribosomal subunit / large ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / ribosome binding / 5S rRNA binding / response to radiation / small ribosomal subunit / protein-containing complex assembly / transferase activity / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / protein dimerization activity / translation / transcription, DNA-templated / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / magnesium ion binding / RNA binding / DNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm
Ribosomal protein L30, conserved site / Ribosomal S11, conserved site / Ribosomal protein S5, N-terminal / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / RNA polymerase Rpb2, OB-fold / Ribosomal protein L2, domain 3 / DNA-directed RNA polymerase, subunit 2 / Transcription antitermination protein, NusG, bacteria, conserved site ...Ribosomal protein L30, conserved site / Ribosomal S11, conserved site / Ribosomal protein S5, N-terminal / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / RNA polymerase Rpb2, OB-fold / Ribosomal protein L2, domain 3 / DNA-directed RNA polymerase, subunit 2 / Transcription antitermination protein, NusG, bacteria, conserved site / K homology domain-like, alpha/beta / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S4, conserved site / Ribosomal protein S2, conserved site / 50S ribosomal protein uL4 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein L25/L23 / DNA-directed RNA polymerase, subunit beta-prime / DNA-directed RNA polymerase, beta subunit, external 1 domain / Translation protein SH3-like domain superfamily / Ribosomal protein L11, bacterial-type / RNA polymerase, N-terminal / NusG, N-terminal / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 3 / Translation protein, beta-barrel domain superfamily / Ribosomal protein L23/L15e core domain superfamily / K homology domain superfamily, prokaryotic type / Ribosomal protein L9/RNase H1, N-terminal / S15/NS1, RNA-binding / DNA-directed RNA polymerase beta subunit, bacterial-type / Ribosomal protein S13-like, H2TH / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / RNA polymerase, alpha subunit, C-terminal / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / Zinc-binding ribosomal protein / DNA-directed RNA polymerase, alpha subunit / RNA polymerase subunit, RPB6/omega / Nucleic acid-binding, OB-fold / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein S3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein S12/S23 / Ribosomal protein L31 type A / RNA-binding domain, S1 / Ribosomal protein L10 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / Ribosomal protein L28/L24 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein L21-like / Ribosomal protein S4/S9 / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / L28p-like / Ribosomal protein L20, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L29/L35 superfamily / RPB6/omega subunit-like superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L5 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein L3, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein L3, bacterial/organelle-type
50S ribosomal protein L21 / 50S ribosomal protein L17 / Transcription termination/antitermination protein NusG / 50S ribosomal protein L23 / 50S ribosomal protein L16 / 50S ribosomal protein L9 / 50S ribosomal protein L14 / 50S ribosomal protein L13 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta' ...50S ribosomal protein L21 / 50S ribosomal protein L17 / Transcription termination/antitermination protein NusG / 50S ribosomal protein L23 / 50S ribosomal protein L16 / 50S ribosomal protein L9 / 50S ribosomal protein L14 / 50S ribosomal protein L13 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit alpha / 50S ribosomal protein L30 / 50S ribosomal protein L22 / 50S ribosomal protein L6 / 30S ribosomal protein S1 / 50S ribosomal protein L18 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L24 / 50S ribosomal protein L4 / 50S ribosomal protein L5 / 50S ribosomal protein L25 / 50S ribosomal protein L31 / 30S ribosomal protein S6 / gb:cp054232.1: / gb:cp054236.1: / 50S ribosomal protein L34 / 50S ribosomal protein L35 / 30S ribosomal protein S4 / 50S ribosomal protein L33 / 30S ribosomal protein S11 / 50S ribosomal protein L10 / 30S ribosomal protein S5 / 50S ribosomal protein L36 / 30S ribosomal protein S18 / 30S ribosomal protein S12 / 30S ribosomal protein S10 / 30S ribosomal protein S19 / 30S ribosomal protein S3 / 30S ribosomal protein S17 / 30S ribosomal protein S14 / 30S ribosomal protein S8 / 30S ribosomal protein S13 / 30S ribosomal protein S9 / 50S ribosomal protein L32 / 30S ribosomal protein S15 / 30S ribosomal protein S21 / 30S ribosomal protein S16 / 30S ribosomal protein S2 / 30S ribosomal protein S20 / 30S ribosomal protein S7 / 50S ribosomal protein L15 / 50S ribosomal protein L11 / 50S ribosomal protein L19 / 50S ribosomal protein L20 / 50S ribosomal protein L27 / 50S ribosomal protein L28 / 50S ribosomal protein L29 / gb:cp035706.1:
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWebster, M.W. / Takacs, M. / Weixlbaumer, A.
Funding support France, 5items
OrganizationGrant numberCountry
European Research Council (ERC)679734 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
French National Research AgencyANR-10-LABX-0030-INRT France
French National Research AgencyANR-10-IDEX-0002-02 France
European Molecular Biology Organization (EMBO)LTF375-2019 France
CitationJournal: Science / Year: 2020
Title: Structural basis of transcription-translation coupling and collision in bacteria.
Authors: Michael William Webster / Maria Takacs / Chengjin Zhu / Vita Vidmar / Ayesha Eduljee / Mo'men Abdelkareem / Albert Weixlbaumer /
Abstract: Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The ...Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here, we present a series of structures representing uncoupled, coupled, and collided expressome states determined by cryo-electron microscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, which stabilizes an otherwise-variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance channel to the RNAP exit channel. In this collided complex, NusG linkage is no longer possible. These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
AA: 16S ribosomal RNA
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein S21
AV: mRNA
AW: tRNA(fmet) P-site
AX: Phe-NH-tRNA(Phe) A-site
AY: 30S ribosomal protein S1
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L9
BI: 50S ribosomal protein L10
BJ: 50S ribosomal protein L11
BK: 50S ribosomal protein L13
BL: 50S ribosomal protein L14
BM: 50S ribosomal protein L15
BN: 50S ribosomal protein L16
BO: 50S ribosomal protein L17
BP: 50S ribosomal protein L18
BQ: 50S ribosomal protein L19
BR: 50S ribosomal protein L20
BS: 50S ribosomal protein L21
BT: 50S ribosomal protein L22
BU: 50S ribosomal protein L23
BV: 50S ribosomal protein L24
BW: 50S ribosomal protein L25
BX: 50S ribosomal protein L27
BY: 50S ribosomal protein L28
BZ: 50S ribosomal protein L29
B1: 50S ribosomal protein L30
B2: 50S ribosomal protein L32
B3: 50S ribosomal protein L33
B4: 50S ribosomal protein L34
B5: 50S ribosomal protein L35
B6: 50S ribosomal protein L36
B7: 50S ribosomal protein L31
CN: Non-template DNA strand
CT: Template DNA strand
CA: DNA-directed RNA polymerase subunit alpha
CB: DNA-directed RNA polymerase subunit alpha
CC: DNA-directed RNA polymerase subunit beta
CD: DNA-directed RNA polymerase subunit beta'
CE: DNA-directed RNA polymerase subunit omega
CF: Transcription termination/antitermination protein NusG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,745,484550
Polymers2,733,41566
Non-polymers12,069484
Water0
1


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

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Components

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RNA chain , 6 types, 6 molecules AAAVAWAXBABB

#1: RNA chain 16S ribosomal RNA /


Mass: 499888.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: CP054232.1
#22: RNA chain mRNA / Messenger RNA


Mass: 17060.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#23: RNA chain tRNA(fmet) P-site


Mass: 24832.918 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)
#24: RNA chain Phe-NH-tRNA(Phe) A-site


Mass: 24751.018 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: GenBank: CP054236.1
#26: RNA chain 23S ribosomal RNA /


Mass: 941820.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#27: RNA chain 5S ribosomal RNA /


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: CP035706.1

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

#2: Protein 30S ribosomal protein S2 /


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3TPN2
#3: Protein 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQX2
#4: Protein 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR62
#5: Protein 30S ribosomal protein S5 /


Mass: 17617.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A090BZW5
#6: Protein 30S ribosomal protein S6 /


Mass: 15197.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: W8T6F0
#7: Protein 30S ribosomal protein S7 / / Small ribosomal subunit protein uS7


Mass: 17637.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#8: Protein 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR12
#9: Protein 30S ribosomal protein S9 /


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SRY2
#10: Protein 30S ribosomal protein S10 /


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQT7
#11: Protein 30S ribosomal protein S11 /


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR57
#12: Protein 30S ribosomal protein S12 /


Mass: 13814.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQR7
#13: Protein 30S ribosomal protein S13 /


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR52
#14: Protein 30S ribosomal protein S14 /


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SR07
#15: Protein 30S ribosomal protein S15 /


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SSQ7
#16: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SYP2
#17: Protein 30S ribosomal protein S17 /


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQY7
#18: Protein 30S ribosomal protein S18 /


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SFP7
#19: Protein 30S ribosomal protein S19 /


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3SQW2
#20: Protein 30S ribosomal protein S20 /


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3TRH7
#21: Protein 30S ribosomal protein S21 /


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3STZ7
#25: Protein 30S ribosomal protein S1 / / Bacteriophage Q beta RNA-directed RNA polymerase subunit I / Small ribosomal subunit protein bS1


Mass: 61238.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG67

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50S ribosomal protein ... , 31 types, 31 molecules BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZB1B2B3B4B5B6B7

#28: Protein 50S ribosomal protein L2 / / ribosomal protein uL2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60422
#29: Protein 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22291.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#30: Protein 50S ribosomal protein L4 / / ribosomal protein uL4


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60723
#31: Protein 50S ribosomal protein L5 / / ribosomal protein uL5


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P62399
#32: Protein 50S ribosomal protein L6 / / ribosomal protein uL6


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG55
#33: Protein 50S ribosomal protein L9 / / ribosomal protein bL9


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R1
#34: Protein 50S ribosomal protein L10 /


Mass: 17736.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A073UC57
#35: Protein 50S ribosomal protein L11 / / ribosomal protein uL11


Mass: 14894.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7J7
#36: Protein 50S ribosomal protein L13 / / ribosomal protein uL13


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA10
#37: Protein 50S ribosomal protein L14 / / ribosomal protein uL14


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3
#38: Protein 50S ribosomal protein L15 / / Large ribosomal subunit protein uL15


Mass: 14994.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02413
#39: Protein 50S ribosomal protein L16 / / Large ribosomal subunit protein uL16


Mass: 15327.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY7
#40: Protein 50S ribosomal protein L17 / / ribosomal protein bL17


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG44
#41: Protein 50S ribosomal protein L18 / / ribosomal protein uL18


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0C018
#42: Protein 50S ribosomal protein L19 / / ribosomal protein bL19


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7K6
#43: Protein 50S ribosomal protein L20 / / ribosomal protein bL20


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L3
#44: Protein 50S ribosomal protein L21 / / ribosomal protein bL21


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG48
#45: Protein 50S ribosomal protein L22 / / ribosomal protein uL22


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P61175
#46: Protein 50S ribosomal protein L23 / / ribosomal protein uL23


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#47: Protein 50S ribosomal protein L24 / / ribosomal protein uL24


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#48: Protein 50S ribosomal protein L25 / / ribosomal protein bL25


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68919
#49: Protein 50S ribosomal protein L27 / / ribosomal protein bL27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#50: Protein 50S ribosomal protein L28 / / ribosomal protein bL28


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M2
#51: Protein 50S ribosomal protein L29 / / ribosomal protein uL29


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M6
#52: Protein 50S ribosomal protein L30 / / ribosomal protein uL30


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG51
#53: Protein 50S ribosomal protein L32 / / ribosomal protein bL32


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N4
#54: Protein 50S ribosomal protein L33 / / ribosomal protein bL33


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7N9
#55: Protein/peptide 50S ribosomal protein L34 / / ribosomal protein bL34


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7P5
#56: Protein 50S ribosomal protein L35 / / Ribosomal protein A / ribosomal protein bL35


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#57: Protein/peptide 50S ribosomal protein L36 /


Mass: 5720.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A2X1PTA3
#58: Protein 50S ribosomal protein L31 /


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: U9XX47

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DNA chain , 2 types, 2 molecules CNCT

#59: DNA chain Non-template DNA strand


Mass: 12063.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#60: DNA chain Template DNA strand


Mass: 11872.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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

#61: Protein DNA-directed RNA polymerase subunit alpha / Polymerase / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 36558.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Plasmid: pEcrpoABC(-XH)Z / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#62: Protein DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150820.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoB, Z5560, ECs4910 / Plasmid: pEcrpoABC(-XH)Z / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8V4, DNA-directed RNA polymerase
#63: Protein DNA-directed RNA polymerase subunit beta' / Polymerase / 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) / Gene: rpoC, Z5561, ECs4911 / Plasmid: pEcrpoABC(-XH)Z / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8T8, DNA-directed RNA polymerase
#64: Protein DNA-directed RNA polymerase subunit omega / Polymerase / 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) / Gene: rpoZ, b3649, JW3624 / Plasmid: pEcrpoABC(-XH)Z / Production host: Escherichia coli (E. coli) / References: UniProt: P0A800, DNA-directed RNA polymerase

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Protein , 1 types, 1 molecules CF

#65: Protein Transcription termination/antitermination protein NusG


Mass: 20502.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nusG,Z5555,ECs4905 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFG1

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Non-polymers , 3 types, 484 molecules

#66: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 479 / Source method: obtained synthetically / Formula: Mg
#67: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#68: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1E. coli 70S-RNAP expressome complex in NusG-coupled stateCOMPLEX#1-#650MULTIPLE SOURCES
270S ribosome within the NusG-coupled expressomeCOMPLEX#1-#21, #25-#581NATURAL
3DNA-directed RNA polymerase within the NusG-coupled expressomeCOMPLEX#23-#24, #61-#651RECOMBINANT
4synthetic mRNA and template DNACOMPLEX#22, #59-#601RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
44synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDPlasmid
23Escherichia coli (E. coli)562pEcrpoABC(-XH)Z
34synthetic construct (others)32630
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESHEPES1
2150 mMPotassium acetateKOAc1
35 mMMagneium acetateMg(OAc)21
410 mMAmmonium chlorideNH4Cl1
52 uMZinc chlorideZnCl21
62 mMDithiothreitolDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K

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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 / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm
Specimen holderModel: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategory
1RELION3.0.4particle selection
2EPUimage acquisition
4Gctf0.56CTF correction
7UCSF Chimeramodel fitting
9PHENIX1.16model refinement
10RELION3.0.4initial Euler assignment
11RELION3.0.4final Euler assignment
13RELION3.0.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 387633
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15327 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model building
IDPDB-ID3D fitting-ID
14YBB1
26ALH1
RefinementCross valid method: NONE

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