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Yorodumi- PDB-7yny: Crystal structure of baculovirus LEF-3 from Helicoverpa armigera ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yny | ||||||
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Title | Crystal structure of baculovirus LEF-3 from Helicoverpa armigera nucleopolyhedrovirus | ||||||
Components | Lef3 | ||||||
Keywords | DNA BINDING PROTEIN / ssDNA / SSB / Baculovirus / Replication | ||||||
Function / homology | Nucleopolyhedrovirus late expression factor 3 / Nucleopolyhedrovirus late expression factor 3 (LEF-3) / regulation of DNA-templated transcription / DNA binding / Lef3 Function and homology information | ||||||
Biological species | Helicoverpa armigera nucleopolyhedrovirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å | ||||||
Authors | Yin, J. / Li, Z. / Cao, S. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: Structural transitions during the cooperative assembly of baculovirus single-stranded DNA-binding protein on ssDNA. Authors: Jiayi Yin / Yan Fu / Guibo Rao / Zhiqiang Li / Kexing Tian / Tingting Chong / Kai Kuang / Manli Wang / Zhihong Hu / Sheng Cao / Abstract: Single-stranded DNA-binding proteins (SSBs) interact with single-stranded DNA (ssDNA) to form filamentous structures with various degrees of cooperativity, as a result of intermolecular interactions ...Single-stranded DNA-binding proteins (SSBs) interact with single-stranded DNA (ssDNA) to form filamentous structures with various degrees of cooperativity, as a result of intermolecular interactions between neighboring SSB subunits on ssDNA. However, it is still challenging to perform structural studies on SSB-ssDNA filaments at high resolution using the most studied SSB models, largely due to the intrinsic flexibility of these nucleoprotein complexes. In this study, HaLEF-3, an SSB protein from Helicoverpa armigera nucleopolyhedrovirus, was used for in vitro assembly of SSB-ssDNA filaments, which were structurally studied at atomic resolution using cryo-electron microscopy. Combined with the crystal structure of ssDNA-free HaLEF-3 octamers, our results revealed that the three-dimensional rearrangement of HaLEF-3 induced by an internal hinge-bending movement is essential for the formation of helical SSB-ssDNA complexes, while the contacting interface between adjacent HaLEF-3 subunits remains basically intact. We proposed a local cooperative SSB-ssDNA binding model, in which, triggered by exposure to oligonucleotides, HaLEF-3 molecules undergo ring-to-helix transition to initiate continuous SSB-SSB interactions along ssDNA. Unique structural features revealed by the assembly of HaLEF-3 on ssDNA suggest that HaLEF-3 may represent a new class of SSB. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yny.cif.gz | 579.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yny.ent.gz | 438 KB | Display | PDB format |
PDBx/mmJSON format | 7yny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yny_validation.pdf.gz | 521.2 KB | Display | wwPDB validaton report |
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Full document | 7yny_full_validation.pdf.gz | 554.2 KB | Display | |
Data in XML | 7yny_validation.xml.gz | 88 KB | Display | |
Data in CIF | 7yny_validation.cif.gz | 116 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/7yny ftp://data.pdbj.org/pub/pdb/validation_reports/yn/7yny | HTTPS FTP |
-Related structure data
Related structure data | 7ypoC 7ypqC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47637.707 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicoverpa armigera nucleopolyhedrovirus Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q91BW6 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.73 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 1,200 mM sodium phosphate monobasic, 800 mM potassium phosphate dibasic, 100 mM CAPS/NaOH, pH 10.5, 200 mM lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 3.51→48.52 Å / Num. obs: 44026 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 133.56 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.28 |
Reflection shell | Resolution: 3.51→3.64 Å / Rmerge(I) obs: 0.737 / Num. unique obs: 4203 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: our cryoEM model Resolution: 3.51→48.52 Å / SU ML: 0.5849 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.5101 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 137.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.51→48.52 Å
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Refine LS restraints |
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LS refinement shell |
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