+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16448 | |||||||||
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Title | Replication Protein A bound to DNA | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Pyrococcus abyssi (archaea) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 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_16448.map.gz | 327.7 MB | EMDB map data format | |
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Header (meta data) | emd-16448-v30.xml emd-16448.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16448_fsc.xml | 14.9 KB | Display | FSC data file |
Images | emd_16448.png | 54.8 KB | ||
Masks | emd_16448_msk_1.map | 347.6 MB | Mask map | |
Others | emd_16448_half_map_1.map.gz emd_16448_half_map_2.map.gz | 322.1 MB 322.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16448 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16448 | HTTPS FTP |
-Validation report
Summary document | emd_16448_validation.pdf.gz | 921.4 KB | Display | EMDB validaton report |
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Full document | emd_16448_full_validation.pdf.gz | 921 KB | Display | |
Data in XML | emd_16448_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | emd_16448_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16448 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16448 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16448.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_16448_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16448_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16448_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 180 KDa |
-Supramolecule #2: RPA 1, 2 and 3
Supramolecule | Name: RPA 1, 2 and 3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
-Supramolecule #3: poly dT
Supramolecule | Name: poly dT / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: RPA1
Macromolecule | Name: RPA1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSVLTKDRII EIIERKTGMS REEIEEEIRK IMEEDPYLSE QGAAALLAER LGIDLIEKEE VSLMRISELY PGMDPREVNV VGRVLKKYPP REYTRKDGSV GRVASLIIYD DSGRARVVLW DAKVSEYYNK IEVGDVIKVL DAQVKESLSG LPELHINFRA RIILNPDDPR ...String: MSVLTKDRII EIIERKTGMS REEIEEEIRK IMEEDPYLSE QGAAALLAER LGIDLIEKEE VSLMRISELY PGMDPREVNV VGRVLKKYPP REYTRKDGSV GRVASLIIYD DSGRARVVLW DAKVSEYYNK IEVGDVIKVL DAQVKESLSG LPELHINFRA RIILNPDDPR VEMIPPLEEV RVATYTRKKI KDIEAGDRFV EVRGTIAKVY RVLTYDACPE CKKKVDYDEG LGVWICPEHG EVQPIKMTIL DFGLDDGTGY IRVTLFGDDA EELLGVSPEE IAEKIKELEE SGLTTKEAAR KLAEDEFYNI IGREIVVRGN VIEDRFLGLI LRASSWEDVD YRREIERIKE ELEKLGVM |
-Macromolecule #2: RPA2
Macromolecule | Name: RPA2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSKKRMPATR LYIKDILEGY FVKSEGDFEP NYLITKYARK VYRAKIVGTV VREPLIAEDE TYGKFQVDDG TGVIWVLGFR DDTKFAKLVR KGDLVQVIGK IAEWRDDKQI LVEGVSKVHP NMWILHRYET LKEKIEHIKK AKIALEIYNQ YGITAKSKVI AKNKGIEEEL ...String: MSKKRMPATR LYIKDILEGY FVKSEGDFEP NYLITKYARK VYRAKIVGTV VREPLIAEDE TYGKFQVDDG TGVIWVLGFR DDTKFAKLVR KGDLVQVIGK IAEWRDDKQI LVEGVSKVHP NMWILHRYET LKEKIEHIKK AKIALEIYNQ YGITAKSKVI AKNKGIEEEL LEVIDELYGI MMEERSIEEP MEELLEEEIP EEKEENELLE KAKEDILNIL RQKRTAISRK YILKKLGDKY DEETIDDAIT ELLAQGEIYE PETGYYKLL |
-Macromolecule #3: RPA3
Macromolecule | Name: RPA3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Pyrococcus abyssi (archaea) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GTGDGSEVQV RRRKPAVERK ISEIREEDTR VSLIGRVIKV DKMDYMFWLD DGTGVAIIES ESDLPKVGQV VRVIGRIIRN EEGIHIYAEV IQDFSDADLE ALEEIRELER KLLPRLEGEI VW |
-Macromolecule #4: poly dT
Macromolecule | Name: poly dT / type: dna / ID: 4 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Sequence | String: TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT |
-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 | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 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 |