+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16445 | |||||||||
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Title | RPA tetrameric supercomplex with AROD-OB-1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA replication / single strand DNA-binding protein / RPA / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information nucleic acid binding / chromosome, telomeric region / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Pyrococcus abyssi (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Madru C / Martinez-Carranza M / Legrand P / Sauguet L | |||||||||
Funding support | France, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: DNA-binding mechanism and evolution of replication protein A. Authors: Clément Madru / Markel Martínez-Carranza / Sébastien Laurent / Alessandra C Alberti / Maelenn Chevreuil / Bertrand Raynal / Ahmed Haouz / Rémy A Le Meur / Marc Delarue / Ghislaine ...Authors: Clément Madru / Markel Martínez-Carranza / Sébastien Laurent / Alessandra C Alberti / Maelenn Chevreuil / Bertrand Raynal / Ahmed Haouz / Rémy A Le Meur / Marc Delarue / Ghislaine Henneke / Didier Flament / Mart Krupovic / Pierre Legrand / Ludovic Sauguet / Abstract: Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in ...Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD (Acidic Rpa1 OB-binding Domain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in eukaryotes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16445.map.gz | 204.1 MB | EMDB map data format | |
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Header (meta data) | emd-16445-v30.xml emd-16445.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16445_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_16445.png | 108.6 KB | ||
Masks | emd_16445_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-16445.cif.gz | 5.9 KB | ||
Others | emd_16445_half_map_1.map.gz emd_16445_half_map_2.map.gz | 200.3 MB 200.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16445 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16445 | HTTPS FTP |
-Validation report
Summary document | emd_16445_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_16445_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_16445_validation.xml.gz | 21 KB | Display | |
Data in CIF | emd_16445_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16445 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16445 | HTTPS FTP |
-Related structure data
Related structure data | 8c5zMC 8aa9C 8aajC 8aasC 8c5yC 8oejC 8oelC 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_16445.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16445_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16445_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16445_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RPA tetrameric supercomplex alternative conformation with AROD-OB-1
Entire | Name: RPA tetrameric supercomplex alternative conformation with AROD-OB-1 |
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Components |
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-Supramolecule #1: RPA tetrameric supercomplex alternative conformation with AROD-OB-1
Supramolecule | Name: RPA tetrameric supercomplex alternative conformation with AROD-OB-1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
Molecular weight | Theoretical: 345 KDa |
-Macromolecule #1: Replication factor A
Macromolecule | Name: Replication factor A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
Molecular weight | Theoretical: 41.008965 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSVLTKDRII EIIERKTGMS REEIEEEIRK IMEEDPYLSE QGAAALLAER LGIDLIEKEE VSLMRISELY PGMDPREVNV VGRVLKKYP PREYTRKDGS VGRVASLIIY DDSGRARVVL WDAKVSEYYN KIEVGDVIKV LDAQVKESLS GLPELHINFR A RIILNPDD ...String: MSVLTKDRII EIIERKTGMS REEIEEEIRK IMEEDPYLSE QGAAALLAER LGIDLIEKEE VSLMRISELY PGMDPREVNV VGRVLKKYP PREYTRKDGS VGRVASLIIY DDSGRARVVL WDAKVSEYYN KIEVGDVIKV LDAQVKESLS GLPELHINFR A RIILNPDD PRVEMIPPLE EVRVATYTRK KIKDIEAGDR FVEVRGTIAK VYRVLTYDAC PECKKKVDYD EGLGVWICPE HG EVQPIKM TILDFGLDDG TGYIRVTLFG DDAEELLGVS PEEIAEKIKE LEESGLTTKE AARKLAEDEF YNIIGREIVV RGN VIEDRF LGLILRASSW EDVDYRREIE RIKEELEKLG VM UniProtKB: Replication factor A |
-Macromolecule #2: RPA32 subunit of the hetero-oligomeric complex involved in homolo...
Macromolecule | Name: RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
Molecular weight | Theoretical: 20.930475 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: KKRMPATRLY IKDILEGYFV KSEGDFEPNY LITKYARKVY RAKIVGTVVR EPLIAEDETY GKFQVDDGTG VIWVLGFRDD TKFAKLVRK GDLVQVIGKI AEWRDDKQIL VEGVSKVHPN MWILHRYETL KEKIEHIKKA KIALEIYNQY GITAKSKVIA K NKGIEEEL LEVIDELYGI MM UniProtKB: RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination |
-Macromolecule #3: RPA14 subunit of the hetero-oligomeric complex involved in homolo...
Macromolecule | Name: RPA14 subunit of the hetero-oligomeric complex involved in homologous recombination type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
Molecular weight | Theoretical: 13.078994 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: RRRKPAVERK ISEIREEDTR VSLIGRVIKV DKMDYMFWLD DGTGVAIIES ESDLPKVGQV VRVIGRIIRN EEGIHIYAEV IQDFSDADL EALEEIRELE RKLLPRLEGE IVW UniProtKB: RPA14 subunit of the hetero-oligomeric complex involved in homologous recombination |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |