[English] 日本語
Yorodumi
- EMDB-31154: Yeast Dmc1 post-synaptic complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31154
TitleYeast Dmc1 post-synaptic complex
Map data3.41 angstrom resolution cryoEM structure of yeast Dmc1-dsDNA post-synaptic complex
Sample
  • Complex: Yeast Dmc1 post-synaptic complex
    • Protein or peptide: HLJ1_G0016300.mRNA.1.CDS.1
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
    • DNA: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsMeiotic recombination protein DMC1 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology:
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsZhao LY / Xu JF / Wang HW
Funding support China, 7 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700654 China
National Natural Science Foundation of China (NSFC)31825009 China
National Natural Science Foundation of China (NSFC)21877069 China
National Natural Science Foundation of China (NSFC)21922704 China
National Natural Science Foundation of China (NSFC)31570754 China
National Natural Science Foundation of China (NSFC)21625302 China
National Natural Science Foundation of China (NSFC)21933010 China
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination.
Authors: Jingfei Xu / Lingyun Zhao / Sijia Peng / Huiying Chu / Rui Liang / Meng Tian / Philip P Connell / Guohui Li / Chunlai Chen / Hong-Wei Wang /
Abstract: Homologous recombination (HR) is a primary DNA double-strand breaks (DSBs) repair mechanism. The recombinases Rad51 and Dmc1 are highly conserved in the RecA family; Rad51 is mainly responsible for ...Homologous recombination (HR) is a primary DNA double-strand breaks (DSBs) repair mechanism. The recombinases Rad51 and Dmc1 are highly conserved in the RecA family; Rad51 is mainly responsible for DNA repair in somatic cells during mitosis while Dmc1 only works during meiosis in germ cells. This spatiotemporal difference is probably due to their distinctive mismatch tolerance during HR: Rad51 does not permit HR in the presence of mismatches, whereas Dmc1 can tolerate certain mismatches. Here, the cryo-EM structures of Rad51-DNA and Dmc1-DNA complexes revealed that the major conformational differences between these two proteins are located in their Loop2 regions, which contain invading single-stranded DNA (ssDNA) binding residues and double-stranded DNA (dsDNA) complementary strand binding residues, stabilizing ssDNA and dsDNA in presynaptic and postsynaptic complexes, respectively. By combining molecular dynamic simulation and single-molecule FRET assays, we identified that V273 and D274 in the Loop2 region of human RAD51 (hRAD51), corresponding to P274 and G275 of human DMC1 (hDMC1), are the key residues regulating mismatch tolerance during strand exchange in HR. This HR accuracy control mechanism provides mechanistic insights into the specific roles of Rad51 and Dmc1 in DNA double-strand break repair and may shed light on the regulatory mechanism of genetic recombination in mitosis and meiosis.
History
DepositionApr 1, 2021-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_31154.png

Downloads & links

-
Map

FileDownload / File: emd_31154.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.41 angstrom resolution cryoEM structure of yeast Dmc1-dsDNA post-synaptic complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 360 pix.
= 369. Å		1.03 Å/pix.
x 360 pix.
= 369. Å		1.03 Å/pix.
x 360 pix.
= 369. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.025 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.043158747 - 0.08828777
Average (Standard dev.)0.00020192064 (±0.0030020077)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 369.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Yeast Dmc1 post-synaptic complex

EntireName: Yeast Dmc1 post-synaptic complex
Components
  • Complex: Yeast Dmc1 post-synaptic complex
    • Protein or peptide: HLJ1_G0016300.mRNA.1.CDS.1
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
    • DNA: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: Yeast Dmc1 post-synaptic complex

SupramoleculeName: Yeast Dmc1 post-synaptic complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: 3.41 angstrom cryoEM structure of yeast Dmc1-dsDNA post-synaptic complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Macromolecule #1: HLJ1_G0016300.mRNA.1.CDS.1

MacromoleculeName: HLJ1_G0016300.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 36.657539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVTGTEIDS DTAKNILSVD ELQNYGINAS DLQKLKSGGI YTVNTVLSTT RRHLCKIKGL SEVKVEKIKE AAGKIIQVGF IPATVQLDI RQRVYSLSTG SKQLDSILGG GIMTMSITEV FGEFRCGKTQ MSHTLCVTTQ LPREMGGGEG KVAYIDTEGT F RPERIKQI ...String:
MSVTGTEIDS DTAKNILSVD ELQNYGINAS DLQKLKSGGI YTVNTVLSTT RRHLCKIKGL SEVKVEKIKE AAGKIIQVGF IPATVQLDI RQRVYSLSTG SKQLDSILGG GIMTMSITEV FGEFRCGKTQ MSHTLCVTTQ LPREMGGGEG KVAYIDTEGT F RPERIKQI AEGYELDPES CLANVSYARA LNSEHQMELV EQLGEELSSG DYRLIVVDSI MANFRVDYCG RGELSERQQK LN QHLFKLN RLAEEFNVAV FLTNQVQSDP GASALFASAD GRKPIGGHVL AHASATRILL RKGRGDERVA KLQDSPDMPE KEC VYVIGE KGITDSSD

UniProtKB: UNIPROTKB: A0A6L0Z498

-
Macromolecule #2: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')

MacromoleculeName: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 2.692778 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

-
Macromolecule #3: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 2.773904 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 15.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 56.77 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71192
Startup modelType of model: EMDB MAP
EMDB ID:

9566

Final angle assignmentType: NOT APPLICABLE

+
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