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- EMDB-10548: bacterial RNA polymerase rrnTAC (state1) -

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Basic information

Entry
Database: EMDB / ID: EMD-10548
Titlebacterial RNA polymerase rrnTAC (state1)
Map data
Sample
  • Complex: bacterial rRNA transcription anti-termination complex
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 / bacterial-type RNA polymerase core enzyme 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 / bacterial-type RNA polymerase core enzyme binding / rRNA primary transcript binding / transcription elongation-coupled chromatin remodeling / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / transcription antitermination factor activity, RNA binding / phosphatidylinositol phosphate biosynthetic process / bacterial-type flagellum-dependent cell motility / nitrate assimilation / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / transcription elongation factor complex / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / maintenance of translational fidelity / DNA-templated transcription termination / DNA-templated transcription initiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribonucleoside binding / ribosomal small subunit assembly / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytosolic small ribosomal subunit / ribosome biogenesis / protein complex oligomerization / cytoplasmic translation / small ribosomal subunit / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / tRNA binding / rRNA binding / protein dimerization activity / ribosome / structural constituent of ribosome / translation / DNA-binding transcription factor activity / protein domain specific binding / nucleotide binding / response to antibiotic / DNA-templated transcription / regulation of 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. / Transcription termination factor NusA, C-terminal duplication / Inositol monophosphatase, metal-binding site ...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. / Transcription termination factor NusA, C-terminal duplication / Inositol monophosphatase, metal-binding site / 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 / 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 / Type-1 KH domain profile. / DNA repair Rad51/transcription factor NusA, alpha-helical / 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 / Ribosomal protein S4, bacterial-type / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / 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 / Ribosomal protein S10 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta
Similarity search - Domain/homology
30S ribosomal protein S10 / Transcription termination/antitermination protein NusA / Transcription antitermination protein NusB / Inositol-1-monophosphatase / 30S ribosomal protein S4 / Transcription antitermination protein NusB / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega ...30S ribosomal protein S10 / Transcription termination/antitermination protein NusA / Transcription antitermination protein NusB / Inositol-1-monophosphatase / 30S ribosomal protein S4 / Transcription antitermination protein NusB / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsHilal T / Huang Y / Wahl MC
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)RTG 2473-1 Germany
German Research Foundation (DFG)INST 130/1014-1 FUGG Germany
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 16, 2019-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tqo
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10548.png

Downloads & links

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Map

FileDownload / File: emd_10548.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.24 Å
Density
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-3.688598 - 10.990046
Average (Standard dev.)-0.0122485105 (±0.45420298)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z372.000372.000372.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-3.68910.990-0.012

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Supplemental data

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Sample components

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Entire : bacterial rRNA transcription anti-termination complex

EntireName: bacterial rRNA transcription anti-termination complex
Components
  • Complex: bacterial rRNA transcription anti-termination complex

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Supramolecule #1: bacterial rRNA transcription anti-termination complex

SupramoleculeName: bacterial rRNA transcription anti-termination complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 633 kDa/nm

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 10 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 31000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-50 / Number real images: 2706 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 195463
CTF correctionSoftware - Name: cisTEM
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cisTEM
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 61750
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6tqo:
rrn anti-termination complex

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