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- EMDB-16089: Human full length RAD52 undecamer -

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Basic information

Entry
Database: EMDB / ID: EMD-16089
TitleHuman full length RAD52 undecamer
Map dataHuman full length RAD52 cryo-electron density map
Sample
  • Complex: Human full length RAD52
    • Protein or peptide: DNA repair protein RAD52 homolog
  • Ligand: water
KeywordsDNA repair protein / oligomeric structure / DNA BINDING PROTEIN
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 / HDR through MMEJ (alt-NHEJ) / regulation of nucleotide-excision repair / 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 / HDR through MMEJ (alt-NHEJ) / regulation of nucleotide-excision repair / 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: 2.2 Å
AuthorsMarotta R / Balboni B / Girotto S / Cavalli A
Funding supportEuropean Union, Italy, 2 items
OrganizationGrant numberCountry
iNEXT-Discovery15983European Union
Italian Association for Cancer ResearchIG 2018 Id.21386 Italy
Citation
Journal: Commun Biol / Year: 2024
Title: An integrative structural study of the human full-length RAD52 at 2.2 Å resolution.
Authors: Beatrice Balboni / Roberto Marotta / Francesco Rinaldi / Giulia Milordini / Giulia Varignani / Stefania Girotto / Andrea Cavalli /
Abstract: Human RAD52 (RAD52) is a DNA-binding protein involved in many DNA repair mechanisms and genomic stability maintenance. In the last few years, this protein was discovered to be a promising novel ...Human RAD52 (RAD52) is a DNA-binding protein involved in many DNA repair mechanisms and genomic stability maintenance. In the last few years, this protein was discovered to be a promising novel pharmacological target for anticancer strategies. Although the interest in RAD52 has exponentially grown in the previous decade, most information about its structure and mechanism still needs to be elucidated. Here, we report the 2.2 Å resolution cryo-EM reconstruction of the full-length RAD52 (FL-RAD52) protein. This allows us to describe the hydration shell of the N-terminal region of FL-RAD52, which is structured in an undecamer ring. Water molecules coordinate with protein residues to promote stabilization inside and among the protomers and within the inner DNA binding cleft to drive protein-DNA recognition. Additionally, through a multidisciplinary approach involving SEC-SAXS and computational methods, we comprehensively describe the highly flexible and dynamic organization of the C-terminal portion of FL-RAD52. This work discloses unprecedented structural details on the FL-RAD52, which will be critical for characterizing its mechanism of action and inhibitor development, particularly in the context of novel approaches to synthetic lethality and anticancer drug discovery.
#1: Journal: Biorxiv / Year: 2023
Title: Novel structural insights on full-length human RAD52: Cryo-EM and beyond
Authors: Balboni B / Marotta R / Rinaldi F / Girotto S / Cavalli A
History
DepositionNov 4, 2022-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16089.png

Downloads & links

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Map

FileDownload / File: emd_16089.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman full length RAD52 cryo-electron density map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 210 pix.
= 153.51 Å		0.73 Å/pix.
x 210 pix.
= 153.51 Å		0.73 Å/pix.
x 210 pix.
= 153.51 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-9.473584000000001 - 17.225204000000002
Average (Standard dev.)-0.010555187 (±0.91932017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 153.51 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human full-length RAD52 half cryo-electron density map 1

Fileemd_16089_half_map_1.map
AnnotationHuman full-length RAD52 half cryo-electron density map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human full-length RAD52 half cryo-electron density map 2

Fileemd_16089_half_map_2.map
AnnotationHuman full-length RAD52 half cryo-electron density map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human full length RAD52

EntireName: Human full length RAD52
Components
  • Complex: Human full length RAD52
    • Protein or peptide: DNA repair protein RAD52 homolog
  • Ligand: water

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Supramolecule #1: Human full length RAD52

SupramoleculeName: Human full length RAD52 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: N-terminal 6xHis-RAD52 recombinant protein
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 650 KDa

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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: 48.044637 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHENL YFQGMSGTEE AILGGRDSHP AAGGGSVLCF GQCQYTAEEY QAIQKALRQR LGPEYISSRM AGGGQKVCYI EGHRVINLA NEMFGYNGWA HSITQQNVDF VDLNNGKFYV GVCAFVRVQL KDGSYHEDVG YGVSEGLKSK ALSLEKARKE A VTDGLKRA ...String:
MHHHHHHENL YFQGMSGTEE AILGGRDSHP AAGGGSVLCF GQCQYTAEEY QAIQKALRQR LGPEYISSRM AGGGQKVCYI EGHRVINLA NEMFGYNGWA HSITQQNVDF VDLNNGKFYV GVCAFVRVQL KDGSYHEDVG YGVSEGLKSK ALSLEKARKE A VTDGLKRA LRSFGNALGN CILDKDYLRS LNKLPRQLPL EVDLTKAKRQ DLEPSVEEAR YNSCRPNMAL GHPQLQQVTS PS RPSHAVI PADQDCSSRS LSSSAVESEA THQRKLRQKQ LQQQFRERME KQQVRVSTPS AEKSEAAPPA PPVTHSTPVT VSE PLLEKD FLAGVTQELI KTLEDNSEKW AVTPDAGDGV VKPSSRADPA QTSDTLALNN QMVTQNRTPH SVCHQKPQAK SGSW DLQTY SADQRTTGNW ESHRKSQDMK KRKYDPS

UniProtKB: DNA repair protein RAD52 homolog

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 498 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.7 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 318.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 17400 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 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: 4124609
Startup modelType of model: OTHER
Details: 3D initial model algorithm as implemented in Relion 4.0
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C11 (11 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 835808
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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