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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Mfd DNA complex | |||||||||
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![]() | DNA TRANSLOCASE / TRANSCRIPTION-COUPLED DNA REPAIR / HELICASE / ATPASE / DNA BINDING PROTEIN / HYDROLASE-DNA COMPLEX / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | ![]() transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase core enzyme binding / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / DNA repair complex / transcription-coupled nucleotide-excision repair / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / damaged DNA binding / hydrolase activity / DNA repair ...transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase core enzyme binding / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / DNA repair complex / transcription-coupled nucleotide-excision repair / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / damaged DNA binding / hydrolase activity / DNA repair / DNA damage response / regulation of DNA-templated transcription / DNA binding / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.2 Å | |||||||||
![]() | Oakley AJ / Xu Z-Q | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of transcription modulation by the transcription-repair coupling factor. Authors: Bishnu P Paudel / Zhi-Qiang Xu / Slobodan Jergic / Aaron J Oakley / Nischal Sharma / Simon H J Brown / James C Bouwer / Peter J Lewis / Nicholas E Dixon / Antoine M van Oijen / Harshad Ghodke / ![]() Abstract: Elongation by RNA polymerase is dynamically modulated by accessory factors. The transcription-repair coupling factor (TRCF) recognizes paused/stalled RNAPs and either rescues transcription or ...Elongation by RNA polymerase is dynamically modulated by accessory factors. The transcription-repair coupling factor (TRCF) recognizes paused/stalled RNAPs and either rescues transcription or initiates transcription termination. Precisely how TRCFs choose to execute either outcome remains unclear. With Escherichia coli as a model, we used single-molecule assays to study dynamic modulation of elongation by Mfd, the bacterial TRCF. We found that nucleotide-bound Mfd converts the elongation complex (EC) into a catalytically poised state, presenting the EC with an opportunity to restart transcription. After long-lived residence in this catalytically poised state, ATP hydrolysis by Mfd remodels the EC through an irreversible process leading to loss of the RNA transcript. Further, biophysical studies revealed that the motor domain of Mfd binds and partially melts DNA containing a template strand overhang. The results explain pathway choice determining the fate of the EC and provide a molecular mechanism for transcription modulation by TRCF. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 34.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.3 KB 16.3 KB | Display Display | ![]() |
Images | ![]() | 29.8 KB | ||
Filedesc metadata | ![]() | 6.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 391.5 KB | Display | ![]() |
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Full document | ![]() | 391.1 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ssgMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.74 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : mfd complex with DNA
Entire | Name: mfd complex with DNA |
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Components |
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-Supramolecule #1: mfd complex with DNA
Supramolecule | Name: mfd complex with DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 130 KDa |
-Macromolecule #1: Transcription-repair-coupling factor
Macromolecule | Name: Transcription-repair-coupling factor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 130.152422 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPEQYRYTLP VKAGEQRLLG ELTGAACATL VAEIAERHAG PVVLIAPDMQ NALRLHDEIS QFTDQMVMNL ADWETLPYDS FSPHQDIIS SRLSTLYQLP TMQRGVLIVP VNTLMQRVCP HSFLHGHALV MKKGQRLSRD ALRTQLDSAG YRHVDQVMEH G EYATRGAL ...String: MPEQYRYTLP VKAGEQRLLG ELTGAACATL VAEIAERHAG PVVLIAPDMQ NALRLHDEIS QFTDQMVMNL ADWETLPYDS FSPHQDIIS SRLSTLYQLP TMQRGVLIVP VNTLMQRVCP HSFLHGHALV MKKGQRLSRD ALRTQLDSAG YRHVDQVMEH G EYATRGAL LDLFPMGSEL PYRLDFFDDE IDSLRVFDVD SQRTLEEVEA INLLPAHEFP TDKAAIELFR SQWRDTFEVK RD PEHIYQQ VSKGTLPAGI EYWQPLFFSE PLPPLFSYFP ANTLLVNTGD LETSAERFQA DTLARFENRG VDPMRPLLPP QSL WLRVDE LFSELKNWPR VQLKTEHLPT KAANANLGFQ KLPDLAVQAQ QKAPLDALRK FLETFDGPVV FSVESEGRRE ALGE LLARI KIAPQRIMRL DEASDRGRYL MIGAAEHGFV DTVRNLALIC ESDLLGERVA RRRQDSRRTI NPDTLIRNLA ELHIG QPVV HLEHGVGRYA GMTTLEAGGI TGEYLMLTYA NDAKLYVPVS SLHLISRYAG GAEENAPLHK LGGDAWSRAR QKAAEK VRD VAAELLDIYA QRAAKEGFAF KHDREQYQLF CDSFPFETTP DQAQAINAVL SDMCQPLAMD RLVCGDVGFG KTEVAMR AA FLAVDNHKQV AVLVPTTLLA QQHYDNFRDR FANWPVRIEM ISRFRSAKEQ TQILAEVAEG KIDILIGTHK LLQSDVKF K DLGLLIVDEE HRFGVRHKER IKAMRANVDI LTLTATPIPR TLNMAMSGMR DLSIIATPPA RRLAVKTFVR EYDSMVVRE AILREILRGG QVYYLYNDVE NIQKAAERLA ELVPEARIAI GHGQMREREL ERVMNDFHHQ RFNVLVCTTI IETGIDIPTA NTIIIERAD HFGLAQLHQL RGRVGRSHHQ AYAWLLTPHP KAMTTDAQKR LEAIASLEDL GAGFALATHD LEIRGAGELL G EEQSGSME TIGFSLYMEL LENAVDALKA GREPSLEDLT SQQTEVELRM PSLLPDDFIP DVNTRLSFYK RIASAKTENE LE EIKVELI DRFGLLPDPA RTLLDIARLR QQAQKLGIRK LEGNEKGGVI EFAEKNHVNP AWLIGLLQKQ PQHYRLDGPT RLK FIQDLS ERKTRIEWVR QFMRELEENA IA UniProtKB: Transcription-repair-coupling factor |
-Macromolecule #2: DNA (5'-D(P*TP*TP*GP*CP*CP*TP*CP*GP*CP*TP*GP*CP*CP*A)-3')
Macromolecule | Name: DNA (5'-D(P*TP*TP*GP*CP*CP*TP*CP*GP*CP*TP*GP*CP*CP*A)-3') type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 17.597205 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DG)(DC)(DC)(DT)(DC)(DG) ...String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DG)(DC)(DC)(DT)(DC)(DG)(DC)(DT) (DG)(DC)(DC)(DG)(DT)(DC)(DG)(DC)(DC)(DA) |
-Macromolecule #3: DNA (5'-D(P*TP*GP*GP*CP*GP*GP*CP*GP*AP*GP*GP*C)-3')
Macromolecule | Name: DNA (5'-D(P*TP*GP*GP*CP*GP*GP*CP*GP*AP*GP*GP*C)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 5.607617 KDa |
Sequence | String: (DT)(DG)(DG)(DC)(DG)(DA)(DC)(DG)(DG)(DC) (DA)(DG)(DC)(DG)(DA)(DG)(DG)(DC) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.6 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | ADP, NaF and AlCl3 were added to final concentrations of 2, 5 and 0.5 mM, respectively. |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 472 / Average exposure time: 50.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |