+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34430 | ||||||||||||||||||||||||
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Title | Cryo-EM structure of the human RAD52 protein | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
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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 | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | ||||||||||||||||||||||||
Authors | Kinoshita C / Takizawa Y / Saotome M / Ogino S / Kurumizaka H / Kagawa W | ||||||||||||||||||||||||
Funding support | Japan, 7 items
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Citation | Journal: FEBS Open Bio / Year: 2023 Title: The cryo-EM structure of full-length RAD52 protein contains an undecameric ring. Authors: Chiaki Kinoshita / Yoshimasa Takizawa / Mika Saotome / Shun Ogino / Hitoshi Kurumizaka / Wataru Kagawa / Abstract: The human RAD52 protein, which forms an oligomeric ring structure, is involved in DNA double-strand break repair. The N-terminal half of RAD52 is primarily responsible for self-oligomerisation and ...The human RAD52 protein, which forms an oligomeric ring structure, is involved in DNA double-strand break repair. The N-terminal half of RAD52 is primarily responsible for self-oligomerisation and DNA binding. Crystallographic studies have revealed the detailed structure of the N-terminal half. However, only low-resolution structures have been reported for the full-length protein, and thus the structural role of the C-terminal half in self-oligomerisation has remained elusive. In this study, we determined the solution structure of the human RAD52 protein by cryo-electron microscopy (cryo-EM), at an average resolution of 3.5 Å. The structure revealed an undecameric ring that is nearly identical to the crystal structures of the N-terminal half. The cryo-EM map for the C-terminal half was poorly defined, indicating that the region is intrinsically disordered. The present cryo-EM structure provides important insights into the mechanistic roles played by the N-terminal and C-terminal halves of RAD52 during DNA double-strand break repair. | ||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34430.map.gz | 2.1 MB | EMDB map data format | |
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Header (meta data) | emd-34430-v30.xml emd-34430.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34430_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_34430.png | 231.2 KB | ||
Others | emd_34430_half_map_1.map.gz emd_34430_half_map_2.map.gz | 23.5 MB 23.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34430 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34430 | HTTPS FTP |
-Related structure data
Related structure data | 8h1pMC 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_34430.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34430_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34430_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RAD52
Entire | Name: RAD52 |
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Components |
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-Supramolecule #1: RAD52
Supramolecule | Name: RAD52 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-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: 46.514934 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSHMSGTEEA ILGGRDSHPA AGGGSVLCFG QCQYTAEEYQ AIQKALRQRL GPEYISSRMA GGGQKVCYIE GHRVINLANE MFGYNGWAH SITQQNVDFV DLNNGKFYVG VCAFVRVQLK DGSYHEDVGY GVSEGLKSKA LSLEKARKEA VTDGLKRALR S FGNALGNC ...String: GSHMSGTEEA ILGGRDSHPA AGGGSVLCFG QCQYTAEEYQ AIQKALRQRL GPEYISSRMA GGGQKVCYIE GHRVINLANE MFGYNGWAH SITQQNVDFV DLNNGKFYVG VCAFVRVQLK DGSYHEDVGY GVSEGLKSKA LSLEKARKEA VTDGLKRALR S FGNALGNC ILDKDYLRSL NKLPRQLPLE VDLTKAKRQD LEPSVEEARY NSCRPNMALG HPQLQQVTSP SRPSHAVIPA DQ DCSSRSL SSSAVESEAT HQRKLRQKQL QQQFRERMEK QQVRVSTPSA EKSEAAPPAP PVTHSTPVTV SEPLLEKDFL AGV TQELIK TLEDNSEKWA VTPDAGDGVV KPSSRADPAQ TSDTLALNNQ MVTQNRTPHS VCHQKPQAKS GSWDLQTYSA DQRT TGNWE SHRKSQDMKK RKYDPS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-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: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |