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- EMDB-11795: MutS-MutL in clamp state (kinked clamp domain) -

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Basic information

Entry
Database: EMDB / ID: EMD-11795
TitleMutS-MutL in clamp state (kinked clamp domain)
Map data
Sample
  • Complex: MutS loaded on DNA substrate with one central mismatched basepair in the presence of AMP-PNP
    • Complex: DNA mismatch repair protein MutS and DNA mismatch repair endonuclease MutL
      • Protein or peptide: DNA mismatch repair protein MutS
      • Protein or peptide: DNA mismatch repair protein MutL
    • Complex: DNA
      • DNA: DNA (30-MER)
      • DNA: DNA (30-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsDNA Mismatch Repair MutS / DNA BINDING PROTEIN
Function / homology
Function and homology information


single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity ...single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding / DNA damage response / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein MutS / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like ...DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein MutS / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / 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 MutS family / 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA mismatch repair protein MutL / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsFernandez-Leiro R / Bhairosing-Kok D
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-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
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  • Surface view with fitted model
  • Atomic models: PDB-7aic
  • Surface level: 0.1
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Structure viewerEM map:
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Supplemental images

emd_11795.png

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Map

FileDownload / File: emd_11795.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.76 Å/pix.
x 192 pix.
= 337.92 Å		1.76 Å/pix.
x 192 pix.
= 337.92 Å		1.76 Å/pix.
x 192 pix.
= 337.92 Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.24942265 - 0.40202865
Average (Standard dev.)0.000030618256 (±0.008344241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 337.91998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.761.761.76
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z337.920337.920337.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.2490.4020.000

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Supplemental data

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Mask #1

Fileemd_11795_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_11795_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11795_half_map_2.map
Projections & Slices
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Sample components

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Entire : MutS loaded on DNA substrate with one central mismatched basepair...

EntireName: MutS loaded on DNA substrate with one central mismatched basepair in the presence of AMP-PNP
Components
  • Complex: MutS loaded on DNA substrate with one central mismatched basepair in the presence of AMP-PNP
    • Complex: DNA mismatch repair protein MutS and DNA mismatch repair endonuclease MutL
      • Protein or peptide: DNA mismatch repair protein MutS
      • Protein or peptide: DNA mismatch repair protein MutL
    • Complex: DNA
      • DNA: DNA (30-MER)
      • DNA: DNA (30-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: MutS loaded on DNA substrate with one central mismatched basepair...

SupramoleculeName: MutS loaded on DNA substrate with one central mismatched basepair in the presence of AMP-PNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 280 KDa

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Supramolecule #2: DNA mismatch repair protein MutS and DNA mismatch repair endonucl...

SupramoleculeName: DNA mismatch repair protein MutS and DNA mismatch repair endonuclease MutL
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: synthetic construct (others)

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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 (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 95.269625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSAIENFDAH TPMMQQYLRL KAQHPEILLF YRMGDFYELF YDDAKRASQL LDISLTKRGA SAGEPIPMAG IPYHAVENYL AKLVNQGES VAIAEQIGDP ATSKGPVERK VVRIVTPGTI SDEALLQERQ DNLLAAIWQD SKGFGYATLD ISSGRFRLSE P ADRETMAA ...String:
MSAIENFDAH TPMMQQYLRL KAQHPEILLF YRMGDFYELF YDDAKRASQL LDISLTKRGA SAGEPIPMAG IPYHAVENYL AKLVNQGES VAIAEQIGDP ATSKGPVERK VVRIVTPGTI SDEALLQERQ DNLLAAIWQD SKGFGYATLD ISSGRFRLSE P ADRETMAA ELQRTNPAEL LYAEDFAEMS LIEGRRGLRR RPLWEFEIDT ARQQLNLQFG TRDLVGFGVE NAPRGLSAAG AL LQYAKCT QRTTLPHIRS ITMEREQDSI IMDAATRRNL EITQNLAGGA ENTLASVLDS 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 TLNYTSPTFI DKPGIRITEG RHPVVEQVLN EPFIANPLNL SPQRRMLIIT GPNMGGKSTY MRQTALIALM AYIGSYV PA QKVEIGPIDR IFTRVGAADD LASGRSTFMV EMTETANILH NATEYSLVLM DEIGRGTSTY DGLSLAWAVA ENLANKIK A LTLFATHYFE LTQLPEKMEG VANVHLDALE HGDTIAFMHS VQDGAASKSY GLAVAALAGV PKEVIKRARQ KLRELESIS PNAAATQVDG TQMSLLSVPE ETSPAVEALE NLDPRSLTPR QALEWIYRLK SLV

UniProtKB: DNA mismatch repair protein MutS

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Macromolecule #2: DNA mismatch repair protein MutL

MacromoleculeName: DNA mismatch repair protein MutL / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 39.248535 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MPIQVLPPQL ANQIAAGEVV ERPASVVKEL VENSLDAGAT RIDIDIERGG AKLIRIRDNG SGIKKDELA LALARHATSK IASLDDLEAI ISLGFRGEAL ASISSVSRLT LTSRTAEQQE AWQAYAEGRD MCVTVKPAAH P VGTTLEVL ...String:
MGSSHHHHHH SSGLVPRGSH MPIQVLPPQL ANQIAAGEVV ERPASVVKEL VENSLDAGAT RIDIDIERGG AKLIRIRDNG SGIKKDELA LALARHATSK IASLDDLEAI ISLGFRGEAL ASISSVSRLT LTSRTAEQQE AWQAYAEGRD MCVTVKPAAH P VGTTLEVL DLFYNTPARR KFLRTEKTEF NHIDEIIRRI ALARFDVTIN LSHNGKIVRQ YRAVPEGGQK ERRLGAILGT AF LEQALAI EWQHGDLTLR GWVADPNHTT PALAEIQYFY VNGRMMRDRL INHAIRQAYE DKLGADQQPA FVLYLEIDPH QVD VNVHPA KHEVRFHQSR LVHDFIYQGV LSVLQ

UniProtKB: DNA mismatch repair protein MutL

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Macromolecule #3: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.303989 KDa
SequenceString:
(DA)(DT)(DG)(DC)(DC)(DT)(DA)(DT)(DA)(DG) (DG)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DG)(DG) (DG)(DT)(DA)(DC)(DC)(DG)(DC)(DT)(DG) (DA)

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Macromolecule #4: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.143893 KDa
SequenceString:
(DT)(DC)(DA)(DG)(DC)(DG)(DG)(DT)(DA)(DC) (DC)(DC)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DC) (DC)(DT)(DA)(DT)(DA)(DG)(DG)(DC)(DA) (DT)

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Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHepes
50.0 mMPotasium Glutamate
2.0 mMTEMED
1.0 mMATP
0.006 w/vTween-20
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+AMP-PNP prior to grid preparation

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
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: 1-40 / Number grids imaged: 1 / Number real images: 2351 / Average exposure time: 12.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 290291
Startup modelType of model: OTHER / Details: Ab Initio Relion
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 32308
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5akb


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial Jelly Body refinement Final refinement with proSmart restraints
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-7aic:
MutS-MutL in clamp state (kinked clamp domain)

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