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- EMDB-34011: Cryo-EM structure of one baculovirus LEF-3 molecule in complex wi... -
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Open data
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Basic information
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Title | Cryo-EM structure of one baculovirus LEF-3 molecule in complex with ssDNA | |||||||||
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![]() | 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![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Fu Y / Rao G / Yin J / Li Z / Cao S | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 49.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15 KB 15 KB | Display Display | ![]() |
Images | ![]() | 135.6 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Others | ![]() ![]() | 48.8 MB 48.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ypqMC ![]() 7ynyC ![]() 7ypoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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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 |
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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: ![]() |
-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: ![]() |
Molecular weight | Theoretical: 47.637707 KDa |
Recombinant expression | Organism: ![]() ![]() |
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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![]() | single particle reconstruction |
Aggregation state | helical array |
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Sample preparation
Buffer | pH: 6.3 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
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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 |