[English] 日本語
Yorodumi
- EMDB-13255: The structure of E. coli MutL bound to a 3' resected DNA end -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13255
TitleThe structure of E. coli MutL bound to a 3' resected DNA end
Map data
Sample
  • Complex: E. coli MutL N-terminal dimer bound to a 3' resected DNA end
    • Complex: 3' resected DNA end
      • DNA: Template strand
      • DNA: Primer strand
    • Complex: E. coli MutL N-terminal dimer
      • Protein or peptide: DNA mismatch repair protein MutL
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsDNA mismatch repair / Protein-DNA complex / 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 / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / DNA binding ...single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / mismatch repair complex / regulation of DNA recombination / nucleotide-excision repair, DNA duplex unwinding / mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / 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 / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / 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 / 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
Similarity search - Domain/homology
DNA mismatch repair protein MutL
Similarity search - Component
Biological speciesDNA molecule (others) / Escherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBorsellini A / Lamers MH
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITNEuropean Union
CitationJournal: Nucleic Acids Res / Year: 2022
Title: MutL binds to 3' resected DNA ends and blocks DNA polymerase access.
Authors: Alessandro Borsellini / Joyce H G Lebbink / Meindert H Lamers /
Abstract: DNA mismatch repair removes mis-incorporated bases after DNA replication and reduces the error rate a 100-1000-fold. After recognition of a mismatch, a large section of up to a thousand nucleotides ...DNA mismatch repair removes mis-incorporated bases after DNA replication and reduces the error rate a 100-1000-fold. After recognition of a mismatch, a large section of up to a thousand nucleotides is removed from the daughter strand followed by re-synthesis. How these opposite activities are coordinated is poorly understood. Here we show that the Escherichia coli MutL protein binds to the 3' end of the resected strand and blocks access of Pol I and Pol III. The cryo-EM structure of an 85-kDa MutL-DNA complex, determined to 3.7 Å resolution, reveals a unique DNA binding mode that positions MutL at the 3' end of a primer-template, but not at a 5' resected DNA end or a blunt DNA end. Hence, our work reveals a novel role for MutL in the final stages of mismatch repair by preventing premature DNA synthesis during removal of the mismatched strand.
History
DepositionJul 23, 2021-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13255.png

Downloads & links

-
Map

FileDownload / File: emd_13255.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 219.904 Å		0.86 Å/pix.
x 256 pix.
= 219.904 Å		0.86 Å/pix.
x 256 pix.
= 219.904 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.859 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.03163788 - 0.06550156
Average (Standard dev.)0.000099354096 (±0.0013708891)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 219.904 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : E. coli MutL N-terminal dimer bound to a 3' resected DNA end

EntireName: E. coli MutL N-terminal dimer bound to a 3' resected DNA end
Components
  • Complex: E. coli MutL N-terminal dimer bound to a 3' resected DNA end
    • Complex: 3' resected DNA end
      • DNA: Template strand
      • DNA: Primer strand
    • Complex: E. coli MutL N-terminal dimer
      • Protein or peptide: DNA mismatch repair protein MutL
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: E. coli MutL N-terminal dimer bound to a 3' resected DNA end

SupramoleculeName: E. coli MutL N-terminal dimer bound to a 3' resected DNA end
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

-
Supramolecule #2: 3' resected DNA end

SupramoleculeName: 3' resected DNA end / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: DNA molecule (others)

-
Supramolecule #3: E. coli MutL N-terminal dimer

SupramoleculeName: E. coli MutL N-terminal dimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
Macromolecule #1: DNA mismatch repair protein MutL

MacromoleculeName: DNA mismatch repair protein MutL / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 68.005508 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPIQVLPPQL ANQIAAGEVV ERPASVVKEL VENSLDAGAT RIDIDIERGG AKLIRIRDNG CGIKKDELAL ALARHATSKI ASLDDLEAI ISLGFRGEAL ASISSVSRLT LTSRTAEQQE AWQAYAEGRD MNVTVKPAAH PVGTTLEVLD LFYNTPARRK F LRTEKTEF ...String:
MPIQVLPPQL ANQIAAGEVV ERPASVVKEL VENSLDAGAT RIDIDIERGG AKLIRIRDNG CGIKKDELAL ALARHATSKI ASLDDLEAI ISLGFRGEAL ASISSVSRLT LTSRTAEQQE AWQAYAEGRD MNVTVKPAAH PVGTTLEVLD LFYNTPARRK F LRTEKTEF NHIDEIIRRI ALARFDVTIN LSHNGKIVRQ YRAVPEGGQK ERRLGAICGT AFLEQALAIE WQHGDLTLRG WV ADPNHTT PALAEIQYCY VNGRMMRDRL INHAIRQACE DKLGADQQPA FVLYLEIDPH QVDVNVHPAK HEVRFHQSRL VHD FIYQGV LSVLQQQLET PLPLDDEPQP APRSIPENRV AAGRNHFAEP AAREPVAPRY TPAPASGSRP AAPWPNAQPG YQKQ QGEVY RQLLQTPAPM QKLKAPEPQE PALAANSQSF GRVLTIVHSD CALLERDGNI SLLSLPVAER WLRQAQLTPG EAPVC AQPL LIPLRLKVSA EEKSALEKAQ SALAELGIDF QSDAQHVTIR AVPLPLRQQN LQILIPELIG YLAKQSVFEP GNIAQW IAR NLMSEHAQWS MAQAITLLAD VERLCPQLVK TPPGGLLQSV DLHPAIKALK DE

UniProtKB: DNA mismatch repair protein MutL

-
Macromolecule #2: Template strand

MacromoleculeName: Template strand / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 6.841428 KDa
SequenceString:
(DG)(DC)(DT)(DG)(DG)(DA)(DG)(DG)(DC)(DT) (DA)(DA)(DG)(DC)(DT)(DA)(DA)(DG)(DC)(DT) (DG)(DA)

-
Macromolecule #3: Primer strand

MacromoleculeName: Primer strand / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 3.941584 KDa
SequenceString:
(DT)(DC)(DA)(DG)(DC)(DT)(DT)(DA)(DG)(DC) (DT)(DT)(DA)

-
Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / 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

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 8.5
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3tris
150.0 mMNaClsodium chloride
5.0 mMMgCl2magnesium chloride
2.0 mMC4H10O2S2Dithiothreitol
0.01 %C58H114O26tween20
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 76 % / Chamber temperature: 277.15 K / Instrument: LEICA PLUNGER

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 539000 / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 539000
Startup modelType of model: INSILICO MODEL
In silico model: model generated with initial model job type in RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 149000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

+
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