+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16914 | |||||||||
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Title | Cryo-EM structure of the DnaD-NTD tetramer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Replication helicase loading / small cryo-EM structure / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacillus subtilis (bacteria) / Bacillus subtilis subsp. subtilis str. 168 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.47 Å | |||||||||
Authors | Winterhalter C / Pelliciari S / Cronin N / Costa TRD / Murray H / Ilangovan A | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: The DNA replication initiation protein DnaD recognises a specific strand of the Bacillus subtilis chromosome origin. Authors: Charles Winterhalter / Simone Pelliciari / Daniel Stevens / Stepan Fenyk / Elie Marchand / Nora B Cronin / Panos Soultanas / Tiago R D Costa / Aravindan Ilangovan / Heath Murray / Abstract: Genome replication is a fundamental biological activity shared by all organisms. Chromosomal replication proceeds bidirectionally from origins, requiring the loading of two helicases, one for each ...Genome replication is a fundamental biological activity shared by all organisms. Chromosomal replication proceeds bidirectionally from origins, requiring the loading of two helicases, one for each replisome. However, the molecular mechanisms underpinning helicase loading at bacterial chromosome origins (oriC) are unclear. Here we investigated the essential DNA replication initiation protein DnaD in the model organism Bacillus subtilis. A set of DnaD residues required for ssDNA binding was identified, and photo-crosslinking revealed that this ssDNA binding region interacts preferentially with one strand of oriC. Biochemical and genetic data support the model that DnaD recognizes a new single-stranded DNA (ssDNA) motif located in oriC, the DnaD Recognition Element (DRE). Considered with single particle cryo-electron microscopy (cryo-EM) imaging of DnaD, we propose that the location of the DRE within oriC orchestrates strand-specific recruitment of helicase during DNA replication initiation. These findings significantly advance our mechanistic understanding of bidirectional replication from a bacterial chromosome origin. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16914.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-16914-v30.xml emd-16914.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16914_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_16914.png | 33.7 KB | ||
Filedesc metadata | emd-16914.cif.gz | 5.2 KB | ||
Others | emd_16914_half_map_1.map.gz emd_16914_half_map_2.map.gz | 59.5 MB 59.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16914 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16914 | HTTPS FTP |
-Validation report
Summary document | emd_16914_validation.pdf.gz | 727 KB | Display | EMDB validaton report |
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Full document | emd_16914_full_validation.pdf.gz | 726.6 KB | Display | |
Data in XML | emd_16914_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_16914_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16914 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16914 | HTTPS FTP |
-Related structure data
Related structure data | 8ojjMC 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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-Map
File | Download / File: emd_16914.map.gz / Format: CCP4 / Size: 64 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: 0.831 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_16914_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16914_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homo Tetrameric complex of DnaD N-terminal domain
Entire | Name: Homo Tetrameric complex of DnaD N-terminal domain |
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Components |
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-Supramolecule #1: Homo Tetrameric complex of DnaD N-terminal domain
Supramolecule | Name: Homo Tetrameric complex of DnaD N-terminal domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
-Macromolecule #1: DNA replication protein DnaD
Macromolecule | Name: DNA replication protein DnaD / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain: 168 |
Molecular weight | Theoretical: 27.675715 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKKQQFIDMQ EQGTSTIPNL LLTHYKQLGL NETELILLLK IKMHLEKGSY FPTPNQLQEG MSISVEECTN RLRMFIQKGF LFIEECEDQ NGIKFEKYSL QPLWGKLYEY IQLAQNQTQE RKAEGEQKSL YTIFEEEFAR PLSPLECETL AIWQDQDQHD A QLIKHALK ...String: MKKQQFIDMQ EQGTSTIPNL LLTHYKQLGL NETELILLLK IKMHLEKGSY FPTPNQLQEG MSISVEECTN RLRMFIQKGF LFIEECEDQ NGIKFEKYSL QPLWGKLYEY IQLAQNQTQE RKAEGEQKSL YTIFEEEFAR PLSPLECETL AIWQDQDQHD A QLIKHALK EAVLSGKLSF RYIDRILFEW KKNGLKTVEQ AKIHSQKFRR VQAKQNEPQK EYKRQVPFYN WLEQ UniProtKB: DNA replication protein DnaD |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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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 (6k x 4k) / Average electron dose: 50.0 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: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8ojj: |