[English] 日本語
Yorodumi
- EMDB-11791: MutS in Scanning state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11791
TitleMutS in Scanning stateMutS-1
Map data
Sample
  • Complex: MutS loaded on matched DNA in the presence of ATP
    • Complex: DNA mismatch repair protein MutS
      • Protein or peptide: DNA mismatch repair protein MutS
    • Complex: DNA
      • DNA: DNA (5'-D(P*CP*TP*AP*TP*AP*GP*GP*GP*CP*GP*AP*AP*TP*TP*GP*GP*GP*TP*AP*CP*CP*G)-3')
      • DNA: DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*AP*AP*TP*TP*CP*GP*CP*CP*CP*TP*AP*TP*AP*G)-3')
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Function / homology
Function and homology information


mismatched DNA binding / mismatch repair / damaged DNA binding / ATP binding
Similarity search - Function
DNA mismatch repair protein MutS / DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV ...DNA mismatch repair protein MutS / DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV / MutS domain III / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsFernandez-Leiro R / Bhairosing-Kok D / Sixma TK / Lamers MH
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105197143 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: The selection process of licensing a DNA mismatch for repair.
Authors: Rafael Fernandez-Leiro / Doreth Bhairosing-Kok / Vladislav Kunetsky / Charlie Laffeber / Herrie H Winterwerp / Flora Groothuizen / Alexander Fish / Joyce H G Lebbink / Peter Friedhoff / ...Authors: Rafael Fernandez-Leiro / Doreth Bhairosing-Kok / Vladislav Kunetsky / Charlie Laffeber / Herrie H Winterwerp / Flora Groothuizen / Alexander Fish / Joyce H G Lebbink / Peter Friedhoff / Titia K Sixma / Meindert H Lamers /
Abstract: DNA mismatch repair detects and removes mismatches from DNA by a conserved mechanism, reducing the error rate of DNA replication by 100- to 1,000-fold. In this process, MutS homologs scan DNA, ...DNA mismatch repair detects and removes mismatches from DNA by a conserved mechanism, reducing the error rate of DNA replication by 100- to 1,000-fold. In this process, MutS homologs scan DNA, recognize mismatches and initiate repair. How the MutS homologs selectively license repair of a mismatch among millions of matched base pairs is not understood. Here we present four cryo-EM structures of Escherichia coli MutS that provide snapshots, from scanning homoduplex DNA to mismatch binding and MutL activation via an intermediate state. During scanning, the homoduplex DNA forms a steric block that prevents MutS from transitioning into the MutL-bound clamp state, which can only be overcome through kinking of the DNA at a mismatch. Structural asymmetry in all four structures indicates a division of labor between the two MutS monomers. Together, these structures reveal how a small conformational change from the homoduplex- to heteroduplex-bound MutS acts as a licensing step that triggers a dramatic conformational change that enables MutL binding and initiation of the repair cascade.
History
DepositionSep 26, 2020-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateApr 28, 2021-
Current statusApr 28, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ai5
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ai5
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11791.png

Downloads & links

-
Map

FileDownload / File: emd_11791.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 240 pix.
= 280.8 Å		1.17 Å/pix.
x 240 pix.
= 280.8 Å		1.17 Å/pix.
x 240 pix.
= 280.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.17 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.224611 - 0.52721256
Average (Standard dev.)0.0008876156 (±0.015754499)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 280.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.171.171.17
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z280.800280.800280.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.2250.5270.001

-
Supplemental data

-
Mask #1

Fileemd_11791_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_11791_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_11791_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MutS loaded on matched DNA in the presence of ATP

EntireName: MutS loaded on matched DNA in the presence of ATP
Components
  • Complex: MutS loaded on matched DNA in the presence of ATP
    • Complex: DNA mismatch repair protein MutS
      • Protein or peptide: DNA mismatch repair protein MutS
    • Complex: DNA
      • DNA: DNA (5'-D(P*CP*TP*AP*TP*AP*GP*GP*GP*CP*GP*AP*AP*TP*TP*GP*GP*GP*TP*AP*CP*CP*G)-3')
      • DNA: DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*AP*AP*TP*TP*CP*GP*CP*CP*CP*TP*AP*TP*AP*G)-3')
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: MutS loaded on matched DNA in the presence of ATP

SupramoleculeName: MutS loaded on matched DNA in the presence of ATP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 190 KDa

-
Supramolecule #2: DNA mismatch repair protein MutS

SupramoleculeName: DNA mismatch repair protein MutS / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

-
Macromolecule #1: DNA mismatch repair protein MutS

MacromoleculeName: DNA mismatch repair protein MutS / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 95.397898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSAIENFDAH TPMMQQYLRL KAQHPEILLF YRMGDFYELF YDDAKRASQL LDISLTKRGA SAGEPIPMAG IPYHAVENYL AKLVNQGES VAICEQIGDP ATSKGPVERK VVRIVTPGTI SDEALLQERQ DNLLAAIWQD SKGFGYATLD ISSGRFRLSE P ADRETMAA ...String:
MSAIENFDAH TPMMQQYLRL KAQHPEILLF YRMGDFYELF YDDAKRASQL LDISLTKRGA SAGEPIPMAG IPYHAVENYL AKLVNQGES VAICEQIGDP ATSKGPVERK VVRIVTPGTI SDEALLQERQ DNLLAAIWQD SKGFGYATLD ISSGRFRLSE P ADRETMAA ELQRTNPAEL LYAEDFAEMS LIEGRRGLRR RPLWEFEIDT ARQQLNLQFG TRDLVGFGVE NAPRGLCAAG CL LQYAKDT QRTTLPHIRS ITMEREQDSI IMDAATRRNL EITQNLAGGA ENTLASVLDC TVTPMGSRML KRWLHMPVRD TRV LLERQQ TIGALQDFTA GLQPVLRQVG DLERILARLA LRTARPRDLA RMRHAFQQLP ELRAQLETVD SAPVQALREK MGEF AELRD LLERAIIDTP PVLVRDGGVI ASGYNEELDE WRALADGATD YLERLEVRER ERTGLDTLKV GFNAVHGYYI QISRG QSHL APINYMRRQT LKNAERYIIP ELKEYEDKVL TSKGKALALE KQLYEELFDL LLPHLEALQQ SASALAELDV LVNLAE RAY TLNYTCPTFI DKPGIRITEG RHPVVEQVLN EPFIANPLNL SPQRRMLIIT GPNMGGKSTY MRQTALIALM AYIGSYV PA QKVEIGPIDR IFTRVGAADD LASGRSTFMV EMTETANILH NATEYSLVLM DEIGRGTSTY DGLSLAWACA ENLANKIK A LTLFATHYFE LTQLPEKMEG VANVHLDALE HGDTIAFMHS VQDGAASKSY GLAVAALAGV PKEVIKRARQ KLRELESIS PNAAATQVDG TQMSLLSVPE ETSPAVEALE NLDPRSLTPR QALEWIYRLK SLV

-
Macromolecule #2: DNA (5'-D(P*CP*TP*AP*TP*AP*GP*GP*GP*CP*GP*AP*AP*TP*TP*GP*GP*GP*TP...

MacromoleculeName: DNA (5'-D(P*CP*TP*AP*TP*AP*GP*GP*GP*CP*GP*AP*AP*TP*TP*GP*GP*GP*TP*AP*CP*CP*G)-3')
type: dna / ID: 2
Details: Plasmid DNA molecule (pRC1765), sequence in structure unidentified
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.832414 KDa
SequenceString:
(DC)(DT)(DA)(DT)(DA)(DG)(DG)(DG)(DC)(DG) (DA)(DA)(DT)(DT)(DG)(DG)(DG)(DT)(DA)(DC) (DC)(DG)

-
Macromolecule #3: DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*AP*AP*TP*TP*CP*GP*CP*CP*CP*TP...

MacromoleculeName: DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*AP*AP*TP*TP*CP*GP*CP*CP*CP*TP*AP*TP*AP*G)-3')
type: dna / ID: 3
Details: Plasmid DNA molecule (pRC1765), sequence in structure unidentified
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.672318 KDa
SequenceString:
(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DA)(DA) (DT)(DT)(DC)(DG)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DG)

-
Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHepes
50.0 mMPotasium Glutamate
2.0 mMTEMEDTetramethylethylenediamine
1.0 mMATPAdenosine triphosphate
0.006 w/vTween-20
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging.
DetailsProtein sample was purified over a gel filtration column and mixed with DNA+ATP prior to grid preparation

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
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 - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2351 / Average exposure time: 12.0 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 229664
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: Ab Initio Relion
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 36682
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

1e3m

DetailsInitial Jelly Body refinement Final refinement with proSmart restraints
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-7ai5:
MutS in Scanning state

+
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