+Open data
-Basic information
Entry | Database: PDB / ID: 7ypo | ||||||
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Title | Cryo-EM structure of baculovirus LEF-3 in complex with ssDNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / ssDNA / SSB / Baculovirus | ||||||
Function / homology | Nucleopolyhedrovirus late expression factor 3 / Nucleopolyhedrovirus late expression factor 3 (LEF-3) / regulation of DNA-templated transcription / DNA binding / DNA / DNA (> 10) / Lef3 Function and homology information | ||||||
Biological species | Helicoverpa armigera nucleopolyhedrovirus synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Yin, J. / Fu, Y. / Rao, G. / 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 | 7ypo.cif.gz | 257.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ypo.ent.gz | 204.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ypo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ypo_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7ypo_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7ypo_validation.xml.gz | 46.6 KB | Display | |
Data in CIF | 7ypo_validation.cif.gz | 63.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/7ypo ftp://data.pdbj.org/pub/pdb/validation_reports/yp/7ypo | HTTPS FTP |
-Related structure data
Related structure data | 34010MC 7ynyC 7ypqC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 47637.707 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicoverpa armigera nucleopolyhedrovirus Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q91BW6 #2: DNA chain | | Mass: 8724.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component |
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Source (natural) | Organism: Helicoverpa armigera nucleopolyhedrovirus | ||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21 (bacteria) | ||||||||||||||||||||||||
Buffer solution | pH: 6.3 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -108.281 ° / Axial rise/subunit: 15.105 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 530580 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.02 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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