+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1485 | |||||||||
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Title | The archaeal DNA Ligase-PCNA-DNA complex | |||||||||
Map data | This is a map of DNA ligase-PCNA-DNA complex | |||||||||
Sample |
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Biological species | Pyrococcus furiosus (archaea) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 17.0 Å | |||||||||
Authors | Mayanagi K / Kiyonari S / Ishino Y / Shirai T / Morikawa K | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2009 Title: Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture. Authors: Kouta Mayanagi / Shinichi Kiyonari / Mihoko Saito / Tsuyoshi Shirai / Yoshizumi Ishino / Kosuke Morikawa / Abstract: The 3D structure of the ternary complex, consisting of DNA ligase, the proliferating cell nuclear antigen (PCNA) clamp, and DNA, was investigated by single-particle analysis. This report presents the ...The 3D structure of the ternary complex, consisting of DNA ligase, the proliferating cell nuclear antigen (PCNA) clamp, and DNA, was investigated by single-particle analysis. This report presents the structural view, where the crescent-shaped DNA ligase with 3 distinct domains surrounds the central DNA duplex, encircled by the closed PCNA ring, thus forming a double-layer structure with dual contacts between the 2 proteins. The relative orientations of the DNA ligase domains, which remarkably differ from those of the known crystal structures, suggest that a large domain rearrangement occurs upon ternary complex formation. A second contact was found between the PCNA ring and the middle adenylation domain of the DNA ligase. Notably, the map revealed a substantial DNA tilt from the PCNA ring axis. This structure allows us to propose a switching mechanism for the replication factors operating on the PCNA ring. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1485.map.gz | 209.8 KB | EMDB map data format | |
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Header (meta data) | emd-1485-v30.xml emd-1485.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | 1485.png | 286 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1485 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1485 | HTTPS FTP |
-Validation report
Summary document | emd_1485_validation.pdf.gz | 200.5 KB | Display | EMDB validaton report |
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Full document | emd_1485_full_validation.pdf.gz | 199.6 KB | Display | |
Data in XML | emd_1485_validation.xml.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1485 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1485 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1485.map.gz / Format: CCP4 / Size: 670.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a map of DNA ligase-PCNA-DNA complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Pyrococcus furiosus DNA Ligase bound to PCNA and DNA
Entire | Name: Pyrococcus furiosus DNA Ligase bound to PCNA and DNA |
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Components |
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-Supramolecule #1000: Pyrococcus furiosus DNA Ligase bound to PCNA and DNA
Supramolecule | Name: Pyrococcus furiosus DNA Ligase bound to PCNA and DNA / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Heteropentamer / Number unique components: 3 |
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Molecular weight | Theoretical: 160 KDa Method: One DNA Ligase binds to three PCNA and one nicked DNA |
-Macromolecule #1: Pyrococcus furiosus DNA Ligase
Macromolecule | Name: Pyrococcus furiosus DNA Ligase / type: protein_or_peptide / ID: 1 / Name.synonym: DNA Ligase / Recombinant expression: No |
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Source (natural) | Organism: Pyrococcus furiosus (archaea) |
-Macromolecule #2: Proliferating cell nuclear antigen
Macromolecule | Name: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 2 / Name.synonym: PCNA / Number of copies: 3 / Oligomeric state: Trimeric / Recombinant expression: Yes |
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Source (natural) | Organism: Pyrococcus furiosus (archaea) |
Molecular weight | Theoretical: 28 KDa |
-Macromolecule #3: PCNA-nicked DNA
Macromolecule | Name: PCNA-nicked DNA / type: dna / ID: 3 / Name.synonym: DNA / Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: Yes |
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Source (natural) | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 6.5 / Details: 20 mM MES,50 mM NaCl,10 mM MgCl2,0.1 mM ATP |
Staining | Type: NEGATIVE Details: The sample solution was applied to a copper grid supporting a continuous thin-carbon film, left for 1 min, then stained with 3 drops of 2% uranyl acetate, and air dried. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 1010 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 400,000 times magnification |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN / Number real images: 400 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 5.6 mm / Nominal magnification: 400000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN,IMAGIC / Number images used: 19544 |
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-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Details | PDBEntryID_givenInChain. |
Refinement | Space: REAL |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: A |
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Details | PDBEntryID_givenInChain. |
Refinement | Space: REAL |