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- PDB-6tqn: rrn anti-termination complex without S4 -

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Basic information

Entry
Database: PDB / ID: 6tqn
Titlerrn anti-termination complex without S4
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • (Transcription termination/antitermination protein ...) x 2
  • 30S ribosomal protein S10
  • Inositol monophosphatase
  • Inositol-1-monophosphatase
  • Transcription antitermination protein NusB
  • ntDNA
  • rrnGnut
  • tDNA
KeywordsTRANSCRIPTION / rrn / anti-termination complex / RNAP / Nus factors / SuhB
Function / homology
Function and homology information


: / glycerol-2-phosphatase activity / lithium ion binding / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / DNA-templated transcription elongation / inositol metabolic process / rRNA primary transcript binding ...: / glycerol-2-phosphatase activity / lithium ion binding / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / DNA-templated transcription elongation / inositol metabolic process / rRNA primary transcript binding / RNA polymerase complex / transcription elongation-coupled chromatin remodeling / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / phosphatidylinositol phosphate biosynthetic process / protein complex oligomerization / transcription antitermination factor activity, RNA binding / bacterial-type flagellum-dependent cell motility / nitrate assimilation / DNA-directed RNA polymerase complex / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / transcription antitermination / cell motility / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosome biogenesis / small ribosomal subunit / response to heat / cytosolic small ribosomal subunit / protein-containing complex assembly / cytoplasmic translation / intracellular iron ion homeostasis / tRNA binding / protein dimerization activity / ribosome / structural constituent of ribosome / translation / DNA-binding transcription factor activity / protein domain specific binding / response to antibiotic / nucleotide binding / DNA-templated transcription / magnesium ion binding / signal transduction / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Inositol monophosphatase SuhB-like / NusB antitermination factor / NusB/RsmB/TIM44 / NusB family / NusB-like superfamily / Inositol monophosphatase / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase, metal-binding site / Transcription termination factor NusA, C-terminal duplication ...Inositol monophosphatase SuhB-like / NusB antitermination factor / NusB/RsmB/TIM44 / NusB family / NusB-like superfamily / Inositol monophosphatase / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase, metal-binding site / Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / : / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / DNA repair Rad51/transcription factor NusA, alpha-helical / Type-1 KH domain profile. / NusG, N-terminal domain superfamily / Helix-hairpin-helix domain / S1 domain profile. / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / 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 S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S10 / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / 30S ribosomal protein S10 / Transcription termination/antitermination protein NusA / Transcription antitermination protein NusB / Inositol-1-monophosphatase / Transcription antitermination protein NusB / Small ribosomal subunit protein uS10 ...DNA / DNA (> 10) / RNA / RNA (> 10) / 30S ribosomal protein S10 / Transcription termination/antitermination protein NusA / Transcription antitermination protein NusB / Inositol-1-monophosphatase / Transcription antitermination protein NusB / Small ribosomal subunit protein uS10 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta / Nus factor SuhB / Transcription termination/antitermination protein NusA / Transcription termination/antitermination protein NusG / DNA-directed RNA polymerase subunit beta' / Transcription termination/antitermination protein NusG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHuang, Y.H. / Wahl, M.C. / Loll, B. / Hilal, T. / Said, N.
CitationJournal: Mol Cell / Year: 2020
Title: Structure-Based Mechanisms of a Molecular RNA Polymerase/Chaperone Machine Required for Ribosome Biosynthesis.
Authors: Yong-Heng Huang / Tarek Hilal / Bernhard Loll / Jörg Bürger / Thorsten Mielke / Christoph Böttcher / Nelly Said / Markus C Wahl /
Abstract: Bacterial ribosomal RNAs are synthesized by a dedicated, conserved transcription-elongation complex that transcribes at high rates, shields RNA polymerase from premature termination, and supports co- ...Bacterial ribosomal RNAs are synthesized by a dedicated, conserved transcription-elongation complex that transcribes at high rates, shields RNA polymerase from premature termination, and supports co-transcriptional RNA folding, modification, processing, and ribosomal subunit assembly by presently unknown mechanisms. We have determined cryo-electron microscopy structures of complete Escherichia coli ribosomal RNA transcription elongation complexes, comprising RNA polymerase; DNA; RNA bearing an N-utilization-site-like anti-termination element; Nus factors A, B, E, and G; inositol mono-phosphatase SuhB; and ribosomal protein S4. Our structures and structure-informed functional analyses show that fast transcription and anti-termination involve suppression of NusA-stabilized pausing, enhancement of NusG-mediated anti-backtracking, sequestration of the NusG C-terminal domain from termination factor ρ, and the ρ blockade. Strikingly, the factors form a composite RNA chaperone around the RNA polymerase RNA-exit tunnel, which supports co-transcriptional RNA folding and annealing of distal RNA regions. Our work reveals a polymerase/chaperone machine required for biosynthesis of functional ribosomes.
History
DepositionDec 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Dec 16, 2020Group: Database references / Category: citation / Item: _citation.page_last
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
T: Inositol monophosphatase
S: Inositol-1-monophosphatase
A: Transcription termination/antitermination protein NusA
B: Transcription antitermination protein NusB
E: 30S ribosomal protein S10
G: Transcription termination/antitermination protein NusG
U: DNA-directed RNA polymerase subunit alpha
V: DNA-directed RNA polymerase subunit alpha
W: DNA-directed RNA polymerase subunit omega
X: DNA-directed RNA polymerase subunit beta
Y: DNA-directed RNA polymerase subunit beta'
R: rrnGnut
L: tDNA
K: ntDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)602,34719
Polymers602,14314
Non-polymers2045
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 4 molecules TSBE

#1: Protein Inositol monophosphatase


Mass: 29066.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: B9S25_006930 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5B7PBT3, UniProt: P0ADG4*PLUS
#2: Protein Inositol-1-monophosphatase / Inositol-1-phosphatase


Mass: 29537.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: suhB, ssyA, b2533, JW2517 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ADG4, inositol-phosphate phosphatase
#4: Protein Transcription antitermination protein NusB / Antitermination factor NusB


Mass: 15838.161 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nusB, CCU01_023355 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P8C5Y7, UniProt: P0A780*PLUS
#5: Protein 30S ribosomal protein S10


Mass: 12012.884 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsJ, AD31_3986 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A073G203, UniProt: P0A7R5*PLUS

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Transcription termination/antitermination protein ... , 2 types, 2 molecules AG

#3: Protein Transcription termination/antitermination protein NusA


Mass: 55030.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nusA, CCU01_003250 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P8BVH6, UniProt: P0AFF6*PLUS
#6: Protein Transcription termination/antitermination protein NusG


Mass: 20817.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nusG, HMPREF1611_01657 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V0ZS55, UniProt: P0AFG0*PLUS

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

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


Mass: 36558.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10249.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, b3649, JW3624 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A800, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150820.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoB, Z5560, ECs4910 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A8V4, UniProt: P0A8V2*PLUS, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 156748.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, A1WS_04718 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: S1HM87, UniProt: P0A8T7*PLUS, DNA-directed RNA polymerase

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RNA chain , 1 types, 1 molecules R

#11: RNA chain rrnGnut


Mass: 27435.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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DNA chain , 2 types, 2 molecules LK

#12: DNA chain tDNA


Mass: 10645.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#13: DNA chain ntDNA


Mass: 10821.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 2 types, 5 molecules

#14: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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
1rrn anti-termination complex (without S4)COMPLEX#1-#130RECOMBINANT
2rrn anti-termination complex (without S4)COMPLEX#1-#101RECOMBINANT
3rrn anti-termination complex (without S4)COMPLEX#11-#131RECOMBINANT
Molecular weightValue: 650 kDa/nm / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli BL21(DE3) (bacteria)469008
33synthetic construct (others)32630
Buffer solutionpH: 7.5
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 31000 X / Nominal defocus min: 500 nm / Calibrated defocus min: 2500 nm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameCategory
1cryoSPARCparticle selection
2Leginonimage acquisition
4CTFFINDCTF correction
10cryoSPARCinitial Euler assignment
11cisTEMfinal Euler assignment
12cisTEMclassification
13cisTEM3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33821 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00440192
ELECTRON MICROSCOPYf_angle_d0.61754811
ELECTRON MICROSCOPYf_dihedral_angle_d10.64624325
ELECTRON MICROSCOPYf_chiral_restr0.0486292
ELECTRON MICROSCOPYf_plane_restr0.0076832

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