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- EMDB-42066: Cryo-EM density map of a double-ring of human RAD52 in the presen... -

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Basic information

Entry
Database: EMDB / ID: EMD-42066
TitleCryo-EM density map of a double-ring of human RAD52 in the presence of fork DNA
Map dataunshrapenned map from cryoSPARC's homogeneous refinement job
Sample
  • Complex: Cryo-EM density of full length human RAD52 DNA repair protein on a fork DNA
    • Protein or peptide: DNA repair protein RAD52 double ring on a fork DNA
KeywordsDNA repiar protein / Recombination
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.32 Å
AuthorsRazzaghi M / Schnicker NJ / 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
DepositionSep 21, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42066.png

Downloads & links

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Map

FileDownload / File: emd_42066.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunshrapenned map from cryoSPARC's homogeneous refinement job
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 320 pix.
= 306.88 Å		0.96 Å/pix.
x 320 pix.
= 306.88 Å		0.96 Å/pix.
x 320 pix.
= 306.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.959 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.08267888 - 0.20334184
Average (Standard dev.)0.0023378837 (±0.0131631065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 306.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: The half map A downloaded from cryoSPARC's homogeneous refinement job...

Fileemd_42066_half_map_1.map
AnnotationThe half_map_A downloaded from cryoSPARC's homogeneous refinement job and is noisy. The guassian filtering applied using chimerax command as: vop gaussian #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map B downloaded from cryoSPARC's homogeneous refinement job...

Fileemd_42066_half_map_2.map
AnnotationThe half_map_B downloaded from cryoSPARC's homogeneous refinement job and is noisy. The guassian filtering applied using chimerax command as: vop gaussian #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM density of full length human RAD52 DNA repair protein on ...

EntireName: Cryo-EM density of full length human RAD52 DNA repair protein on a fork DNA
Components
  • Complex: Cryo-EM density of full length human RAD52 DNA repair protein on a fork DNA
    • Protein or peptide: DNA repair protein RAD52 double ring on a fork DNA

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Supramolecule #1: Cryo-EM density of full length human RAD52 DNA repair protein on ...

SupramoleculeName: Cryo-EM density of full length human RAD52 DNA repair protein on a fork DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: RAD52 makes a double ring structure in the presence of fork DNA
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA repair protein RAD52 double ring on a fork DNA

MacromoleculeName: DNA repair protein RAD52 double ring on a fork DNA / type: protein_or_peptide / ID: 1
Details: Cryo-EM density map of full length human RAD52 double ring on a fork DNA
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MSGTEEAILG GRDSHPAAGG GSVLCFGQCQ YTAEEYQAIQ KALRQRLGPE YISSRMAGGG QKVCYIEGHR VINLANEMFG YNGWAHSITQ QNVDFVDLNN GKFYVGVCAF VRVQLKDGSY HEDVGYGVSE GLKSKALSLE KARKEAVTDG ...String:
MGSSHHHHHH SSGLVPRGSH MSGTEEAILG GRDSHPAAGG GSVLCFGQCQ YTAEEYQAIQ KALRQRLGPE YISSRMAGGG QKVCYIEGHR VINLANEMFG YNGWAHSITQ QNVDFVDLNN GKFYVGVCAF VRVQLKDGSY HEDVGYGVSE GLKSKALSLE KARKEAVTDG LKRALRSFGN ALGNCILDKD YLRSLNKLPR QLPLEVDLTK AKRQDLEPSV EEARYNSCRP NMALGHPQLQ QVTSPSRPSH AVIPADQDCS SRSLSSSAVE SEATHQRKLR QKQLQQQFRE RMEKQQVRVS TPSAEKSEAA PPAPPVTHST PVTVSEPLLE KDFLAGVTQE LIKTLEDNSE KWAVTPDAGD GVVKPSSRAD PAQTSDTLAL NNQMVTQNRT PHSVCHQKPQ AKSGSWDLQT YSADQRTTGN WESHRKSQDM KKRKYDPS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.26 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
30.0 mMTris
75.0 mMKCl
5.0 mMMgCl2
1.0 mMDTT

Details: 30 mM TrisHCl pH 7.5, 75 mM KCl, 5 mM MgCl2, 1 mM DTT
GridSupport film - Material: CARBON / 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 and prepared fork DNA

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 2 / Number real images: 6093 / Average exposure time: 7.0 sec. / Average electron dose: 50.0 e/Å2 / Details: The images recorded from 2 grids.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 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

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Image processing

Particle selectionNumber selected: 1755381
Details: 2D classes containing double-rings used as a template for Template-based extraction of particles from 2 grids
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 80665
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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