[English] 日本語
Yorodumi
- EMDB-41357: Cryo-EM structure of human full-length RAD52 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41357
TitleCryo-EM structure of human full-length RAD52
Map dataSharpened map used for modeling
Sample
  • Complex: Human RAD52 undecameric structure
    • Protein or peptide: DNA repair protein RAD52 homolog
KeywordsDNA repair / RECOMBINATION
Function / homology
Function and homology information


double-strand break repair via single-strand annealing / DNA double-strand break processing involved in repair via single-strand annealing / DNA recombinase assembly / mitotic recombination / regulation of nucleotide-excision repair / HDR through MMEJ (alt-NHEJ) / HDR through Single Strand Annealing (SSA) / SUMOylation of DNA damage response and repair proteins / protein-DNA complex / double-strand break repair via homologous recombination ...double-strand break repair via single-strand annealing / DNA double-strand break processing involved in repair via single-strand annealing / DNA recombinase assembly / mitotic recombination / regulation of nucleotide-excision repair / HDR through MMEJ (alt-NHEJ) / HDR through Single Strand Annealing (SSA) / SUMOylation of DNA damage response and repair proteins / protein-DNA complex / double-strand break repair via homologous recombination / double-strand break repair / single-stranded DNA binding / cellular response to oxidative stress / DNA recombination / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
DNA recombination/repair protein Rad52 / DNA repair protein Rad52/59/22 / Rad52 family / DNA repair protein Rad52/59/22 superfamily / Rad52/22 family double-strand break repair protein
Similarity search - Domain/homology
DNA repair protein RAD52 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsSchnicker NJ / Razzaghi M / Spies M
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA232425-05 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131704-05 United States
CitationJournal: To Be Published
Title: A double-ring of human RAD52 remodels replication forks restricting fork reversal
Authors: Honda M / Razzaghi M
History
DepositionJul 25, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41357.png

Downloads & links

-
Map

FileDownload / File: emd_41357.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map used for modeling
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 247.65 Å		0.83 Å/pix.
x 300 pix.
= 247.65 Å		0.83 Å/pix.
x 300 pix.
= 247.65 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8255 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0017248477 - 1.7862712
Average (Standard dev.)0.0020899153 (±0.033294037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 247.65001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map 2

Fileemd_41357_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_41357_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human RAD52 undecameric structure

EntireName: Human RAD52 undecameric structure
Components
  • Complex: Human RAD52 undecameric structure
    • Protein or peptide: DNA repair protein RAD52 homolog

-
Supramolecule #1: Human RAD52 undecameric structure

SupramoleculeName: Human RAD52 undecameric structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 532 KDa

-
Macromolecule #1: DNA repair protein RAD52 homolog

MacromoleculeName: DNA repair protein RAD52 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.40402 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MSGTEEAILG GRDSHPAAGG GSVLCFGQCQ YTAEEYQAIQ KALRQRLGPE YISSRMAGGG QKVCYIEGH RVINLANEMF GYNGWAHSIT QQNVDFVDLN NGKFYVGVCA FVRVQLKDGS YHEDVGYGVS EGLKSKALSL E KARKEAVT ...String:
MGSSHHHHHH SSGLVPRGSH MSGTEEAILG GRDSHPAAGG GSVLCFGQCQ YTAEEYQAIQ KALRQRLGPE YISSRMAGGG QKVCYIEGH RVINLANEMF GYNGWAHSIT QQNVDFVDLN NGKFYVGVCA FVRVQLKDGS YHEDVGYGVS EGLKSKALSL E KARKEAVT DGLKRALRSF GNALGNCILD KDYLRSLNKL PRQLPLEVDL TKAKRQDLEP SVEEARYNSC RPNMALGHPQ LQ QVTSPSR PSHAVIPADQ DCSSRSLSSS AVESEATHQR KLRQKQLQQQ FRERMEKQQV RVSTPSAEKS EAAPPAPPVT HST PVTVSE PLLEKDFLAG VTQELIKTLE DNSEKWAVTP DAGDGVVKPS SRADPAQTSD TLALNNQMVT QNRTPHSVCH QKPQ AKSGS WDLQTYSADQ RTTGNWESHR KSQDMKKRKY DPS

UniProtKB: DNA repair protein RAD52 homolog

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.25 mg/mL
BufferpH: 9
Component:
ConcentrationNameFormula
20.0 mMTris
200.0 mMPotassium chlorideKCl
1.0 mMDTT

Details: 20 mM Tris pH 9, 200 mM KCl, 1 mM DTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: -15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsSample was made from frozen protein

-
Electron microscopy

MicroscopeTFS KRIOS
DetailsNo tilt data and tilted data (30 deg) was collected at the same time and processed together
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 11288 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 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: 2261059
Details: Template based picking from no tilt and 30 deg tilt data to deal with preferred orientation
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1kn0

Final reconstructionApplied symmetry - Point group: C11 (11 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 623559
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

1kn0


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial fitting was done in Chimera followed by refinement with Namdinator and then PHENIX alone
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 130.2 / Target criteria: Cross-correlation coefficient
Output model

PDB-8tkq:
Cryo-EM structure of human full-length RAD52

+
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