+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16089 | |||||||||
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Title | Human full length RAD52 undecamer | |||||||||
Map data | Human full length RAD52 cryo-electron density map | |||||||||
Sample |
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Keywords | DNA 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 / regulation of nucleotide-excision repair / mitotic recombination / 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 / regulation of nucleotide-excision repair / mitotic recombination / 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 / cellular response to oxidative stress / single-stranded DNA binding / DNA recombination / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
Authors | Marotta R / Balboni B / Girotto S / Cavalli A | |||||||||
Funding support | European Union, Italy, 2 items
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Citation | 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16089.map.gz | 27.4 MB | EMDB map data format | |
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Header (meta data) | emd-16089-v30.xml emd-16089.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16089_fsc.xml emd_16089_fsc_2.xml | 9.6 KB 7.5 KB | Display Display | FSC data file |
Images | emd_16089.png | 34.9 KB | ||
Filedesc metadata | emd-16089.cif.gz | 5.9 KB | ||
Others | emd_16089_half_map_1.map.gz emd_16089_half_map_2.map.gz | 27.1 MB 27.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16089 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16089 | HTTPS FTP |
-Related structure data
Related structure data | 8bjmMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16089.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Human full length RAD52 cryo-electron density map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.731 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Human full-length RAD52 half cryo-electron density map 1
File | emd_16089_half_map_1.map | ||||||||||||
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Annotation | Human full-length RAD52 half cryo-electron density map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Human full-length RAD52 half cryo-electron density map 2
File | emd_16089_half_map_2.map | ||||||||||||
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Annotation | Human full-length RAD52 half cryo-electron density map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human full length RAD52
Entire | Name: Human full length RAD52 |
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Components |
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-Supramolecule #1: Human full length RAD52
Supramolecule | Name: Human full length RAD52 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: N-terminal 6xHis-RAD52 recombinant protein |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 650 KDa |
-Macromolecule #1: DNA repair protein RAD52 homolog
Macromolecule | Name: DNA repair protein RAD52 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 48.044637 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 498 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 318.15 K / Instrument: FEI VITROBOT MARK IV |
Details | This sample was monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Specialist optics | Energy filter - Name: TFS Selectris X |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 17400 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |