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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22146 | |||||||||
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Title | Structure of Mfd bound to dsDNA | |||||||||
![]() | full map | |||||||||
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![]() | DNA translocase / transcription-coupled DNA repair / helicase / ATPase / DNA BINDING PROTEIN / Hydrolase-DNA complex | |||||||||
Function / homology | ![]() transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase core enzyme binding / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / 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 / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / 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: 5.5 Å | |||||||||
![]() | Zhang C / Lyumkis D | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd. Authors: Christiane Brugger / Cheng Zhang / Margaret M Suhanovsky / David D Kim / Amy N Sinclair / Dmitry Lyumkis / Alexandra M Deaconescu / ![]() Abstract: Mfd couples transcription to nucleotide excision repair, and acts on RNA polymerases when elongation is impeded. Depending on impediment severity, this action results in either transcription ...Mfd couples transcription to nucleotide excision repair, and acts on RNA polymerases when elongation is impeded. Depending on impediment severity, this action results in either transcription termination or elongation rescue, which rely on ATP-dependent Mfd translocation on DNA. Due to its role in antibiotic resistance, Mfd is also emerging as a prime target for developing anti-evolution drugs. Here we report the structure of DNA-bound Mfd, which reveals large DNA-induced structural changes that are linked to the active site via ATPase motif VI. These changes relieve autoinhibitory contacts between the N- and C-termini and unmask UvrA recognition determinants. We also demonstrate that translocation relies on a threonine in motif Ic, widely conserved in translocases, and a family-specific histidine near motif IVa, reminiscent of the "arginine clamp" of RNA helicases. Thus, Mfd employs a mode of DNA recognition that at its core is common to ss/ds translocases that act on DNA or RNA. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.6 KB 20.6 KB | Display Display | ![]() |
Images | ![]() | 119.3 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() | 5.8 MB 5.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 724.7 KB | Display | ![]() |
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Full document | ![]() | 724.3 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xeoMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | full map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half map 1
File | emd_22146_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_22146_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : complex of Mfd bound to dsDNA in the presence of transition state...
Entire | Name: complex of Mfd bound to dsDNA in the presence of transition state analog ADP-AlFx |
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Components |
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-Supramolecule #1: complex of Mfd bound to dsDNA in the presence of transition state...
Supramolecule | Name: complex of Mfd bound to dsDNA in the presence of transition state analog ADP-AlFx type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 150 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: 132.524062 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: HHHHHHSSGL EVLFQGPHMA SMPEQYRYTL PVKAGEQRLL GELTGAACAT LVAEIAERHA GPVVLIAPDM QNALRLHDEI SQFTDQMVM NLADWETLPY DSFSPHQDII SSRLSTLYQL PTMQRGVLIV PVNTLMQRVC PHSFLHGHAL VMKKGQRLSR D ALRTQLDS ...String: HHHHHHSSGL EVLFQGPHMA SMPEQYRYTL PVKAGEQRLL GELTGAACAT LVAEIAERHA GPVVLIAPDM QNALRLHDEI SQFTDQMVM NLADWETLPY DSFSPHQDII SSRLSTLYQL PTMQRGVLIV PVNTLMQRVC PHSFLHGHAL VMKKGQRLSR D ALRTQLDS AGYRHVDQVM EHGEYATRGA LLDLFPMGSE LPYRLDFFDD EIDSLRVFDV DSQRTLEEVE AINLLPAHEF PT DKAAIEL FRSQWRDTFE VKRDPEHIYQ QVSKGTLPAG IEYWQPLFFS EPLPPLFSYF PANTLLVNTG DLETSAERFQ ADT LARFEN RGVDPMRPLL PPQSLWLRVD ELFSELKNWP RVQLKTEHLP TKAANANLGF QKLPDLAVQA QQKAPLDALR KFLE TFDGP VVFSVESEGR REALGELLAR IKIAPQRIMR LDEASDRGRY LMIGAAEHGF VDTVRNLALI CESDLLGERV ARRRQ DSRR TINPDTLIRN LAELHIGQPV VHLEHGVGRY AGMTTLEAGG ITGEYLMLTY ANDAKLYVPV SSLHLISRYA GGAEEN APL HKLGGDAWSR ARQKAAEKVR DVAAELLDIY AQRAAKEGFA FKHDREQYQL FCDSFPFETT PDQAQAINAV LSDMCQP LA MDRLVCGDVG FGKTEVAMRA AFLAVDNHKQ VAVLVPTTLL AQQHYDNFRD RFANWPVRIE MISRFRSAKE QTQILAEV A EGKIDILIGT HKLLQSDVKF KDLGLLIVDE EHRFGVRHKE RIKAMRANVD ILTLTATPIP RTLNMAMSGM RDLSIIATP PARRLAVKTF VREYDSMVVR EAILREILRG GQVYYLYNDV ENIQKAAERL AELVPEARIA IGHGQMRERE LERVMNDFHH QRFNVLVCT TIIETGIDIP TANTIIIERA DHFGLAQLHQ LRGRVGRSHH QAYAWLLTPH PKAMTTDAQK RLEAIASLED L GAGFALAT HDLEIRGAGE LLGEEQSGSM ETIGFSLYME LLENAVDALK AGREPSLEDL TSQQTEVELR MPSLLPDDFI PD VNTRLSF YKRIASAKTE NELEEIKVEL IDRFGLLPDP ARTLLDIARL RQQAQKLGIR KLEGNEKGGV IEFAEKNHVN PAW LIGLLQ KQPQHYRLDG PTRLKFIQDL SERKTRIEWV RQFMRELEEN AIA UniProtKB: Transcription-repair-coupling factor |
-Macromolecule #2: DNA (5'-D(P*AP*GP*GP*AP*TP*AP*CP*TP*TP*AP*CP*AP*GP*CP*CP*AP*TP*C)-3')
Macromolecule | Name: DNA (5'-D(P*AP*GP*GP*AP*TP*AP*CP*TP*TP*AP*CP*AP*GP*CP*CP*AP*TP*C)-3') type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 6.431186 KDa |
Sequence | String: (DA)(DT)(DA)(DG)(DG)(DA)(DT)(DA)(DC)(DT) (DT)(DA)(DC)(DA)(DG)(DC)(DC)(DA)(DT)(DC) (DG) |
-Macromolecule #3: DNA (5'-D(P*GP*AP*TP*GP*GP*CP*TP*GP*TP*AP*AP*GP*TP*AP*TP*CP*CP*T)-3')
Macromolecule | Name: DNA (5'-D(P*GP*AP*TP*GP*GP*CP*TP*GP*TP*AP*AP*GP*TP*AP*TP*CP*CP*T)-3') type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 5.5466 KDa |
Sequence | String: (DG)(DA)(DT)(DG)(DG)(DC)(DT)(DG)(DT)(DA) (DA)(DG)(DT)(DA)(DT)(DC)(DC)(DT) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.0 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER Details: 2.5ul Mfd-DNA complex at 1.0 mg/mL was applied to UltrAuFoil R1.2/1.3 300 mesh grids (Quantifoil) that were previously plasma-cleaned using a Gatan Solarus (75% argon/25% oxygen atmosphere, ...Details: 2.5ul Mfd-DNA complex at 1.0 mg/mL was applied to UltrAuFoil R1.2/1.3 300 mesh grids (Quantifoil) that were previously plasma-cleaned using a Gatan Solarus (75% argon/25% oxygen atmosphere, 15 W for 7s), then manually blotted with a Whatman No. 1 filter paper in a cold room with >80% humidity, and plunged into liquid ethane using a manual plunger. |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-60 / Number real images: 652 / Average exposure time: 6.0 sec. / Average electron dose: 24.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0035 µm / Nominal defocus min: 0.0019 µm / Nominal magnification: 36000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 9822 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: cisTEM |