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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Extended RPA-DNA nucleoprotein filament | |||||||||
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![]() | DNA replication / single strand DNA-binding protein / RPA / DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() response to ionizing radiation / double-strand break repair via homologous recombination / nucleic acid binding / chromosome, telomeric region / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
![]() | Madru C / Martinez-Carranza M / Sauguet L | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 229.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.1 KB 20.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.4 KB | Display | ![]() |
Images | ![]() | 36.2 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 226.9 MB 226.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 897.2 KB | Display | ![]() |
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Full document | ![]() | 896.7 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8oejMC ![]() 8aa9C ![]() 8aajC ![]() 8aasC ![]() 8c5yC ![]() 8c5zC ![]() 8oelC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.76 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
-Entire : RPA bound to a 100-mer poly-dT ssDNA
Entire | Name: RPA bound to a 100-mer poly-dT ssDNA |
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Components |
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-Supramolecule #1: RPA bound to a 100-mer poly-dT ssDNA
Supramolecule | Name: RPA bound to a 100-mer poly-dT ssDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Molecular weight | Theoretical: 180 KDa |
-Supramolecule #2: RPA 1,2,3
Supramolecule | Name: RPA 1,2,3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: poly dT
Supramolecule | Name: poly dT / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Replication factor A
Macromolecule | Name: Replication factor A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 41.008965 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 31.489309 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSKKRMPATR LYIKDILEGY FVKSEGDFEP NYLITKYARK VYRAKIVGTV VREPLIAEDE TYGKFQVDDG TGVIWVLGFR DDTKFAKLV RKGDLVQVIG KIAEWRDDKQ ILVEGVSKVH PNMWILHRYE TLKEKIEHIK KAKIALEIYN QYGITAKSKV I AKNKGIEE ...String: MSKKRMPATR LYIKDILEGY FVKSEGDFEP NYLITKYARK VYRAKIVGTV VREPLIAEDE TYGKFQVDDG TGVIWVLGFR DDTKFAKLV RKGDLVQVIG KIAEWRDDKQ ILVEGVSKVH PNMWILHRYE TLKEKIEHIK KAKIALEIYN QYGITAKSKV I AKNKGIEE ELLEVIDELY GIMMEERSIE EPMEELLEEE IPEEKEENEL LEKAKEDILN ILRQKRTAIS RKYILKKLGD KY DEETIDD AITELLAQGE IYEPETGYYK LL 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: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 14.008925 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GTGDGSEVQV RRRKPAVERK ISEIREEDTR VSLIGRVIKV DKMDYMFWLD DGTGVAIIES ESDLPKVGQV VRVIGRIIRN EEGIHIYAE VIQDFSDADL EALEEIRELE RKLLPRLEGE IVW UniProtKB: RPA14 subunit of the hetero-oligomeric complex involved in homologous recombination |
-Macromolecule #4: poly dT
Macromolecule | Name: poly dT / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 30.374275 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT) ...String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT) |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm |