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Yorodumi- EMDB-34011: Cryo-EM structure of one baculovirus LEF-3 molecule in complex wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34011 | |||||||||
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Title | Cryo-EM structure of one baculovirus LEF-3 molecule in complex with ssDNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ssDNA / SSB / Baculovirus / DNA BINDING PROTEIN | |||||||||
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 / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Fu Y / Rao G / Yin J / Li Z / Cao S | |||||||||
Funding support | China, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34011.map.gz | 49.5 MB | EMDB map data format | |
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Header (meta data) | emd-34011-v30.xml emd-34011.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_34011.png | 135.6 KB | ||
Filedesc metadata | emd-34011.cif.gz | 5.4 KB | ||
Others | emd_34011_half_map_1.map.gz emd_34011_half_map_2.map.gz | 48.8 MB 48.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34011 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34011 | HTTPS FTP |
-Validation report
Summary document | emd_34011_validation.pdf.gz | 733.7 KB | Display | EMDB validaton report |
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Full document | emd_34011_full_validation.pdf.gz | 733.3 KB | Display | |
Data in XML | emd_34011_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_34011_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34011 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34011 | HTTPS FTP |
-Related structure data
Related structure data | 7ypqMC 7ynyC 7ypoC 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_34011.map.gz / Format: CCP4 / Size: 52.7 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: 0.95 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34011_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34011_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Baculovirus LEF-3 in complex with ssDNA
Entire | Name: Baculovirus LEF-3 in complex with ssDNA |
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Components |
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-Supramolecule #1: Baculovirus LEF-3 in complex with ssDNA
Supramolecule | Name: Baculovirus LEF-3 in complex with ssDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: LEF-3
Supramolecule | Name: LEF-3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Helicoverpa armigera nucleopolyhedrovirus |
-Supramolecule #3: ssDNA
Supramolecule | Name: ssDNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: Lef3
Macromolecule | Name: Lef3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Helicoverpa armigera nucleopolyhedrovirus |
Molecular weight | Theoretical: 47.637707 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSMSNMDI SPVKQLIDIE NDDAMNTPEK GMKRPLMRTM SSVEEPQAKM AKLRTLNVK GQLLTKTTMS INNEDYYLFK FLVNNKSIDY YGTQTQFFSL INNKTYELVL QYSRKKLLIK SYEQCEDEDL L MTVCKSVT ...String: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSMSNMDI SPVKQLIDIE NDDAMNTPEK GMKRPLMRTM SSVEEPQAKM AKLRTLNVK GQLLTKTTMS INNEDYYLFK FLVNNKSIDY YGTQTQFFSL INNKTYELVL QYSRKKLLIK SYEQCEDEDL L MTVCKSVT FQEFCANEIK SLLAKFLYGF KIYGSSNVYK LVFVILLEDN NGTINGVQVE MMSDFKRLSG AFKNHVIENE ND LFDCMYK SEEKYFNLYR IKCNHNANNY KSLSLSSNSQ LERLETDDSM FEYEFQYDYT VNISRSNKII QKHRVTGNFT SER NIYQNS DRFVISYDTA NEKIKTSIYN RMENAESKTD YDTSITLKDV TLSQLNSLIE SNLVQVDVYL VTDPNNVKNN VIAG ITKIE IDGTYEPL UniProtKB: Lef3 |
-Macromolecule #2: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Macromolecule | Name: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 3.400317 KDa |
Sequence | String: (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 6.3 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1591740 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |