+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3771 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Three-dimensional reconstruction of FLiP virion | |||||||||
Map data | Reconstruction of Flavobacterium infecting lipid-containing phage FLiP | |||||||||
Sample |
| |||||||||
Function / homology | Major capsid protein Function and homology information | |||||||||
Biological species | unidentified phage (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | De Colibus L / Gillum A / Stuart DI / Huiskonen JT | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: Virus found in a boreal lake links ssDNA and dsDNA viruses. Authors: Elina Laanto / Sari Mäntynen / Luigi De Colibus / Jenni Marjakangas / Ashley Gillum / David I Stuart / Janne J Ravantti / Juha T Huiskonen / Lotta-Riina Sundberg / Abstract: Viruses have impacted the biosphere in numerous ways since the dawn of life. However, the evolution, genetic, structural, and taxonomic diversity of viruses remain poorly understood, in part because ...Viruses have impacted the biosphere in numerous ways since the dawn of life. However, the evolution, genetic, structural, and taxonomic diversity of viruses remain poorly understood, in part because sparse sampling of the virosphere has concentrated mostly on exploring the abundance and diversity of dsDNA viruses. Furthermore, viral genomes are highly diverse, and using only the current sequence-based methods for classifying viruses and studying their phylogeny is complicated. Here we describe a virus, FLiP (-infecting, lipid-containing phage), with a circular ssDNA genome and an internal lipid membrane enclosed in the icosahedral capsid. The 9,174-nt-long genome showed limited sequence similarity to other known viruses. The genetic data imply that this virus might use replication mechanisms similar to those found in other ssDNA replicons. However, the structure of the viral major capsid protein, elucidated at near-atomic resolution using cryo-electron microscopy, is strikingly similar to that observed in dsDNA viruses of the PRD1-adenovirus lineage, characterized by a major capsid protein bearing two β-barrels. The strong similarity between FLiP and another member of the structural lineage, bacteriophage PM2, extends to the capsid organization (pseudo = 21 ) despite the difference in the genetic material packaged and the lack of significant sequence similarity. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3771.map.gz | 1.2 GB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3771-v30.xml emd-3771.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3771_fsc.xml | 24.3 KB | Display | FSC data file |
Images | emd_3771.png | 199.4 KB | ||
Masks | emd_3771_msk_1.map | 1.3 GB | Mask map | |
Others | emd_3771_half_map_1.map.gz emd_3771_half_map_2.map.gz | 1 GB 1 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3771 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3771 | HTTPS FTP |
-Validation report
Summary document | emd_3771_validation.pdf.gz | 516.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3771_full_validation.pdf.gz | 515.7 KB | Display | |
Data in XML | emd_3771_validation.xml.gz | 28.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3771 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3771 | HTTPS FTP |
-Related structure data
Related structure data | 5oacMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_3771.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of Flavobacterium infecting lipid-containing phage FLiP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_3771_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_3771_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_3771_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : unidentified phage
Entire | Name: unidentified phage (virus) |
---|---|
Components |
|
-Supramolecule #1: unidentified phage
Supramolecule | Name: unidentified phage / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: Flavobacterium infecting lipid-containing phage FLiP NCBI-ID: 38018 / Sci species name: unidentified phage / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No |
---|---|
Host (natural) | Organism: Flavobacterium (bacteria) / Strain: sp B330 |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 550.0 Å / T number (triangulation number): 25 |
-Macromolecule #1: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: unidentified phage (virus) |
Molecular weight | Theoretical: 34.533934 KDa |
Sequence | String: MTIKYLSSET EKLMNQTVSG IDVCFTLIGV DDDSFASGSK NDYISDTPKF LDPSNVHIKA TLKRGGKDYV LFSENLALLA KYSTITQGR DQWEEGVKLA AKEMVHLVYI PFSGNTNWPA HINLKDNDVL EVYVNVVRGA YGAELDANAC ICDVRTSPSI G VEKFIPFM ...String: MTIKYLSSET EKLMNQTVSG IDVCFTLIGV DDDSFASGSK NDYISDTPKF LDPSNVHIKA TLKRGGKDYV LFSENLALLA KYSTITQGR DQWEEGVKLA AKEMVHLVYI PFSGNTNWPA HINLKDNDVL EVYVNVVRGA YGAELDANAC ICDVRTSPSI G VEKFIPFM TSYSIRANQA TDLVNLGNDV TRIALLSMTN DVSNIPNAFT DVTLSSDRLD KNFNSNQLIL EHSKCIEDSV RS HANEVDS YLIHEDIEID SAKVHLKMNP AKIRENTIYL VRSHFQTSLE ILQKAVAMEE KHQSADIAKV PAT |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 / Details: 20 mM PBS |
---|---|
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-22 / Average electron dose: 22.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.7 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 160000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 84.31 / Target criteria: Cross-correlation coefficient |
---|---|
Output model | PDB-5oac: |