[English] 日本語
Yorodumi
- EMDB-16432: HSF2BP-BRCA2 ring-shaped complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16432
TitleHSF2BP-BRCA2 ring-shaped complex
Map data
Sample
  • Complex: Complex between HSF2BP and the BRCA2 fragment N2291-Q2342
    • Protein or peptide: HSF2BP
    • Protein or peptide: BRCA2
KeywordsMeiosis / Cancer Antigen / DNA repair / Fertility / Armadillo domain / Intrinsically Disordered Protein / RECOMBINATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsZinn-Justin S / Ghouil R / Miron S / Legrand P / Ouldali M / Winter JM / Ropars V / Arteni AA
Funding supportEuropean Union, France, 2 items
OrganizationGrant numberCountry
iNEXT-Discovery871037European Union
Agence Nationale de la Recherche (ANR)ANR-10-INSB-05 France
CitationJournal: Sci Adv / Year: 2023
Title: BRCA2-HSF2BP oligomeric ring disassembly by BRME1 promotes homologous recombination.
Authors: Rania Ghouil / Simona Miron / Koichi Sato / Dejan Ristic / Sari E van Rossum-Fikkert / Pierre Legrand / Malika Ouldali / Jean-Marie Winter / Virginie Ropars / Gabriel David / Ana-Andreea ...Authors: Rania Ghouil / Simona Miron / Koichi Sato / Dejan Ristic / Sari E van Rossum-Fikkert / Pierre Legrand / Malika Ouldali / Jean-Marie Winter / Virginie Ropars / Gabriel David / Ana-Andreea Arteni / Claire Wyman / Puck Knipscheer / Roland Kanaar / Alex N Zelensky / Sophie Zinn-Justin /
Abstract: In meiotic homologous recombination (HR), BRCA2 facilitates loading of the recombinases RAD51 and DMC1 at the sites of double-strand breaks (DSBs). The HSF2BP-BRME1 complex interacts with BRCA2. Its ...In meiotic homologous recombination (HR), BRCA2 facilitates loading of the recombinases RAD51 and DMC1 at the sites of double-strand breaks (DSBs). The HSF2BP-BRME1 complex interacts with BRCA2. Its absence causes a severe reduction in recombinase loading at meiotic DSB. We previously showed that, in somatic cancer cells ectopically producing HSF2BP, DNA damage can trigger HSF2BP-dependent degradation of BRCA2, which prevents HR. Here, we report that, upon binding to BRCA2, HSF2BP forms octameric rings that are able to interlock into a large ring-shaped 24-mer. Addition of BRME1 leads to dissociation of both of these ring structures and cancels the disruptive effect of HSF2BP on cancer cell resistance to DNA damage. It also prevents BRCA2 degradation during interstrand DNA crosslink repair in egg extracts. We propose that, during meiosis, the control of HSF2BPBRCA2 oligomerization by BRME1 ensures timely assembly of the ring complex that concentrates BRCA2 and controls its turnover, thus promoting HR.
History
DepositionJan 6, 2023-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16432.png

Downloads & links

-
Map

FileDownload / File: emd_16432.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 600 pix.
= 438. Å		0.73 Å/pix.
x 600 pix.
= 438. Å		0.73 Å/pix.
x 600 pix.
= 438. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0272
Minimum - Maximum-0.09052658 - 0.23730436
Average (Standard dev.)-0.000045229586 (±0.006442293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 438.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_16432_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_16432_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex between HSF2BP and the BRCA2 fragment N2291-Q2342

EntireName: Complex between HSF2BP and the BRCA2 fragment N2291-Q2342
Components
  • Complex: Complex between HSF2BP and the BRCA2 fragment N2291-Q2342
    • Protein or peptide: HSF2BP
    • Protein or peptide: BRCA2

-
Supramolecule #1: Complex between HSF2BP and the BRCA2 fragment N2291-Q2342

SupramoleculeName: Complex between HSF2BP and the BRCA2 fragment N2291-Q2342
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The complex contains 24 HSF2BP molecules and 12 BRCA2 peptides
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 900 kDa/nm

-
Macromolecule #1: HSF2BP

MacromoleculeName: HSF2BP / type: protein_or_peptide / ID: 1 / Details: Full-length human HSF2BP / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGEAGAAEEA CRHMGTKEEF VKVRKKDLER LTTEVMQIRD FLPRILNGEV LESFQKLKIV EKNLERKEQ ELEQLKMDCE HFKARLETVQ ADNIREKKEK LALRQQLNEA KQQLLQQAEY C TEMGAAAC TLLWGVSSSE EVVKAILGGD KALKFFSITG QTMESFVKSL ...String:
MGEAGAAEEA CRHMGTKEEF VKVRKKDLER LTTEVMQIRD FLPRILNGEV LESFQKLKIV EKNLERKEQ ELEQLKMDCE HFKARLETVQ ADNIREKKEK LALRQQLNEA KQQLLQQAEY C TEMGAAAC TLLWGVSSSE EVVKAILGGD KALKFFSITG QTMESFVKSL DGDVQELDSD ES QFVFALA GIVTNVAAIA CGREFLVNSS RVLLDTILQL LGDLKPGQCT KLKVLMLMSL YNV SINLKG LKYISESPGF IPLLWWLLSD PDAEVCLHVL RLVQSVVLEP EVFSKSASEF RSSL PLQRI LAMSKSRNPR LQTAAQELLE DLRTLEHNV

-
Macromolecule #2: BRCA2

MacromoleculeName: BRCA2 / type: protein_or_peptide / ID: 2
Details: BRCA2 from N2291 to Q2342 with a C-terminal TEV site (was produced fused to GB1-6His)
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NEFDRIIENQ EKSLKASKST PDGTIKDRRL FMHHVSLEPI TTVPFRTTKE RQENLYFQ

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
25.0 mMTris-HClTris buffer
5.0 mMbeta-mercaptoethanolreducing agent
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsObtained after gel filtration on the complex

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 9531 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 660000
Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 398000
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC
Details: One of these volumes had the shape of an open ring, the two other volumes were well-resolved rings. The 398 000 particles corresponding to these two volumes were used to calculate the final ...Details: One of these volumes had the shape of an open ring, the two other volumes were well-resolved rings. The 398 000 particles corresponding to these two volumes were used to calculate the final cryo-EM map of the complex.
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