[English] 日本語
Yorodumi
- EMDB-13063: The structure of MutS bound to two molecules of AMPPNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13063
TitleThe structure of MutS bound to two molecules of AMPPNP
Map data
Sample
  • Organelle or cellular component: DNA mismatch repair protein MutS
    • Protein or peptide: DNA mismatch repair protein MutS
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Function / homology
Function and homology information


adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding ...adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / 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 / ATP binding / identical protein binding / cytosol
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 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLamers MH / Borsellini A / Friedhoff P / Kunetsky V
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITNEuropean Union
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Cryogenic electron microscopy structures reveal how ATP and DNA binding in MutS coordinates sequential steps of DNA mismatch repair.
Authors: Alessandro Borsellini / Vladislav Kunetsky / Peter Friedhoff / Meindert H Lamers /
Abstract: DNA mismatch repair detects and corrects mismatches introduced during DNA replication. The protein MutS scans for mismatches and coordinates the repair cascade. During this process, MutS undergoes ...DNA mismatch repair detects and corrects mismatches introduced during DNA replication. The protein MutS scans for mismatches and coordinates the repair cascade. During this process, MutS undergoes multiple conformational changes in response to ATP binding, hydrolysis and release, but how ATP induces the various MutS conformations is incompletely understood. Here we present four cryogenic electron microscopy structures of Escherichia coli MutS at sequential stages of the ATP hydrolysis cycle that reveal how ATP binding and hydrolysis induce closing and opening of the MutS dimer, respectively. Biophysical analysis demonstrates how DNA binding modulates the ATPase cycle by prevention of hydrolysis during scanning and mismatch binding, while preventing ADP release in the sliding clamp state. Nucleotide release is achieved when MutS encounters single-stranded DNA that is produced during removal of the daughter strand. The combination of ATP binding and hydrolysis and its modulation by DNA enables MutS to adopt the different conformations needed to coordinate the sequential steps of the mismatch repair cascade.
History
DepositionJun 10, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateOct 26, 2022-
Current statusOct 26, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7oto
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13063.png

Downloads & links

-
Map

FileDownload / File: emd_13063.map.gz / Format: CCP4 / Size: 7.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum0.0 - 0.40731847
Average (Standard dev.)0.005510077 (±0.023252094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin686978
Dimensions149122103
Spacing122149103
CellA: 129.31999 Å / B: 157.93999 Å / C: 109.17999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z122149103
origin x/y/z0.0000.0000.000
length x/y/z129.320157.940109.180
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS696878
NC/NR/NS122149103
D min/max/mean0.0000.4070.006

-
Supplemental data

-
Sample components

-
Entire : DNA mismatch repair protein MutS

EntireName: DNA mismatch repair protein MutS
Components
  • Organelle or cellular component: DNA mismatch repair protein MutS
    • Protein or peptide: DNA mismatch repair protein MutS
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

-
Supramolecule #1: DNA mismatch repair protein MutS

SupramoleculeName: DNA mismatch repair protein MutS / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: MutS bound to two molecules of AMPPNP
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 190 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

-
Macromolecule #1: DNA mismatch repair protein MutS

MacromoleculeName: DNA mismatch repair protein MutS / type: protein_or_peptide / ID: 1 / Details: AMPPNP / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 90.433234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHMSAI ENFDAHTPMM QQYLRLKAQH PEILLFYRMG DFYELFYDDA KRASQLLDIS LTKRGASAGE PIPMAGIPYH AVENYLAKL VNQGESVAIC EQIGDPATSK GPVERKVVRI VTPGTISDEA LLQERQDNLL AAIWQDSKGF GYATLDISSG R FRLSEPAD ...String:
HHHHHHMSAI ENFDAHTPMM QQYLRLKAQH PEILLFYRMG DFYELFYDDA KRASQLLDIS LTKRGASAGE PIPMAGIPYH AVENYLAKL VNQGESVAIC EQIGDPATSK GPVERKVVRI VTPGTISDEA LLQERQDNLL AAIWQDSKGF GYATLDISSG R FRLSEPAD RETMAAELQR TNPAELLYAE DFAEMSLIEG RRGLRRRPLW EFEIDTARQQ LNLQFGTRDL VGFGVENAPR GL CAAGCLL QYAKDTQRTT LPHIRSITME REQDSIIMDA ATRRNLEITQ NLAGGAENTL ASVLDCTVTP MGSRMLKRWL HMP VRDTRV LLERQQTIGA LQDFTAGLQP VLRQVGDLER ILARLALRTA RPRDLARMRH AFQQLPELRA QLETVDSAPV QALR EKMGE FAELRDLLER AIIDTPPVLV RDGGVIASGY NEELDEWRAL ADGATDYLER LEVRERERTG LDTLKVGFNA VHGYY IQIS RGQSHLAPIN YMRRQTLKNA ERYIIPELKE YEDKVLTSKG KALALEKQLY EELFDLLLPH LEALQQSASA LAELDV LVN LAERAYTLNY TCPTFIDKPG IRITEGRHPV VEQVLNEPFI ANPLNLSPQR RMLIITGPNM GGKSTYMRQT ALIALMA YI GSYVPAQKVE IGPIDRIFTR VGAADDLASG RSTFMVEMTE TANILHNATE YSLVLMDEIG RGTSTYDGLS LAWACAEN L ANKIKALTLF ATHYFELTQL PEKMEGVANV HLDALEHGDT IAFMHSVQDG AASKSYGLAV AALAGVPKEV IKRARQKLR ELESIS

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.95 mg/mL
BufferpH: 8.5
Component:
ConcentrationFormulaName
20.0 mM2-Amino-2-hydroxymethyl-propane-1,3-dioltris buffer
150.0 mMNaClSodium chloridesodium chloride
2.0 mM1,4-DithiothreitolDTT
5.0 mMMgCl2magnesium chloride
0.01 %C58H114O26Tween20
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0004 kPa
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 57.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 294231
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 147899
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

1e3m

Output model

PDB-7oto:
The structure of MutS bound to two molecules of AMPPNP

+
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