[English] 日本語
Yorodumi
- EMDB-22146: Structure of Mfd bound to dsDNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22146
TitleStructure of Mfd bound to dsDNA
Map datafull map
Sample
  • Complex: complex of Mfd bound to dsDNA in the presence of transition state analog ADP-AlFx
    • Protein or peptide: Transcription-repair-coupling factor
    • DNA: DNA (5'-D(P*AP*GP*GP*AP*TP*AP*CP*TP*TP*AP*CP*AP*GP*CP*CP*AP*TP*C)-3')
    • DNA: DNA (5'-D(P*GP*AP*TP*GP*GP*CP*TP*GP*TP*AP*AP*GP*TP*AP*TP*CP*CP*T)-3')
KeywordsDNA translocase / transcription-coupled DNA repair / helicase / ATPase / DNA BINDING PROTEIN / Hydrolase-DNA complex
Function / homology
Function and homology information


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
: / MFD, D3 domain / : / Transcription-repair coupling factor / Transcription-repair-coupling factor, C-terminal domain / TRCF-like, C-terminal D7 domain / TRCF domain / TRCF / UvrB, interaction domain / UvrB interaction domain ...: / MFD, D3 domain / : / Transcription-repair coupling factor / Transcription-repair-coupling factor, C-terminal domain / TRCF-like, C-terminal D7 domain / TRCF domain / TRCF / UvrB, interaction domain / UvrB interaction domain / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transcription-repair-coupling factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsZhang C / Lyumkis D
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DP5 OD021396 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121975 United States
CitationJournal: Nat Commun / Year: 2020
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
DepositionJun 12, 2020-
Header (metadata) releaseAug 19, 2020-
Map releaseAug 19, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6xeo
  • Surface level: 2.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22146.png

Downloads & links

-
Map

FileDownload / File: emd_22146.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 1.5 / Movie #1: 2.7
Minimum - Maximum-4.0549855 - 10.698584
Average (Standard dev.)0.004318794 (±0.45324782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 276.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z276.000276.000276.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-4.05510.6990.004

-
Supplemental data

-
Half map: half map 1

Fileemd_22146_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_22146_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : complex of Mfd bound to dsDNA in the presence of transition state...

EntireName: complex of Mfd bound to dsDNA in the presence of transition state analog ADP-AlFx
Components
  • Complex: complex of Mfd bound to dsDNA in the presence of transition state analog ADP-AlFx
    • Protein or peptide: Transcription-repair-coupling factor
    • DNA: DNA (5'-D(P*AP*GP*GP*AP*TP*AP*CP*TP*TP*AP*CP*AP*GP*CP*CP*AP*TP*C)-3')
    • DNA: DNA (5'-D(P*GP*AP*TP*GP*GP*CP*TP*GP*TP*AP*AP*GP*TP*AP*TP*CP*CP*T)-3')

-
Supramolecule #1: complex of Mfd bound to dsDNA in the presence of transition state...

SupramoleculeName: complex of Mfd bound to dsDNA in the presence of transition state analog ADP-AlFx
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 150 KDa

-
Macromolecule #1: Transcription-repair-coupling factor

MacromoleculeName: 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
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 132.524062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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')

MacromoleculeName: 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
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.431186 KDa
SequenceString:
(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')

MacromoleculeName: 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
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.5466 KDa
SequenceString:
(DG)(DA)(DT)(DG)(DG)(DC)(DT)(DG)(DT)(DA) (DA)(DG)(DT)(DA)(DT)(DC)(DC)(DT)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloridesodium chloride
20.0 mMMgCl2magnesium chloride
2.0 mMTCEP
20.0 mMTris-HClTris
VitrificationCryogen 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.

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.0035 µm / Nominal defocus min: 0.0019 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM
Final reconstructionApplied 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

-
Atomic model buiding 1

Initial modelPDB ID:

2eyq


Chain - Chain ID: A / Chain - Residue range: 5-1147 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-6xeo:
Structure of Mfd bound to dsDNA

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more