[English] 日本語
Yorodumi- EMDB-17315: In situ cryoEM structure of the Prototype Foamy Virus capsid, hex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17315 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | In situ cryoEM structure of the Prototype Foamy Virus capsid, hexamer 2 localised reconstruction | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | capsid / Gag / foamy virus / hexamer / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information host cytoskeleton / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / host cell / viral nucleocapsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / DNA binding / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Eastern chimpanzee simian foamy virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Calcraft T / Nans A / Rosenthal PB | |||||||||
Funding support | United Kingdom, 1 items
| |||||||||
Citation | Journal: Cell / Year: 2024 Title: Integrated cryoEM structure of a spumaretrovirus reveals cross-kingdom evolutionary relationships and the molecular basis for assembly and virus entry. Authors: Thomas Calcraft / Nicole Stanke-Scheffler / Andrea Nans / Dirk Lindemann / Ian A Taylor / Peter B Rosenthal / Abstract: Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates ...Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates for gene and oncolytic therapies. Structural studies of PFV contribute to the understanding of the mechanisms of FV replication, cell entry and infection, and retroviral evolution. Here we combine cryoEM and cryoET to determine high-resolution in situ structures of the PFV icosahedral capsid (CA) and envelope glycoprotein (Env), including its type III transmembrane anchor and membrane-proximal external region (MPER), and show how they are organized in an integrated structure of assembled PFV particles. The atomic models reveal an ancient retroviral capsid architecture and an unexpected relationship between Env and other class 1 fusion proteins of the Mononegavirales. Our results represent the de novo structure determination of an assembled retrovirus particle. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_17315.map.gz | 116.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-17315-v30.xml emd-17315.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17315_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_17315.png | 107.4 KB | ||
Masks | emd_17315_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-17315.cif.gz | 6.1 KB | ||
Others | emd_17315_half_map_1.map.gz emd_17315_half_map_2.map.gz | 97.6 MB 97.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17315 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17315 | HTTPS FTP |
-Validation report
Summary document | emd_17315_validation.pdf.gz | 983.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_17315_full_validation.pdf.gz | 982.9 KB | Display | |
Data in XML | emd_17315_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_17315_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17315 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17315 | HTTPS FTP |
-Related structure data
Related structure data | 8oznMC 8ozhC 8ozjC 8ozkC 8ozlC 8ozmC 8ozpC 8ozqC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_17315.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_17315_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_17315_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_17315_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Eastern chimpanzee simian foamy virus
Entire | Name: Eastern chimpanzee simian foamy virus |
---|---|
Components |
|
-Supramolecule #1: Eastern chimpanzee simian foamy virus
Supramolecule | Name: Eastern chimpanzee simian foamy virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2170195 / Sci species name: Eastern chimpanzee simian foamy virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
---|
-Macromolecule #1: Gag polyprotein
Macromolecule | Name: Gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Eastern chimpanzee simian foamy virus |
Molecular weight | Theoretical: 70.693414 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MASGSNVEEY ELDVEALVVI LRDRNIPRNP LHGEVIGLRL TEGWWGQIER FQMVRLILQN DDNEPLQRPR YEVIQRAVNP HTMFMISGP LAELQLAFQD LDLPEGPLRF GPLANGHYVQ GDPYSSSYRP VTMAETAQMT RDELEDVLNT QSEIEIQMIN L LELYEVET ...String: MASGSNVEEY ELDVEALVVI LRDRNIPRNP LHGEVIGLRL TEGWWGQIER FQMVRLILQN DDNEPLQRPR YEVIQRAVNP HTMFMISGP LAELQLAFQD LDLPEGPLRF GPLANGHYVQ GDPYSSSYRP VTMAETAQMT RDELEDVLNT QSEIEIQMIN L LELYEVET RALRRQLAER SSTGQGGISP GAPRSRPPVS SFSGLPSLPS IPGIHPRAPS PPRATSTPGN IPWSLGDDNP PS SSFPGPS QPRVSFHPGN PFVEEEGHRP RSQSRERRRE ILPAPVPSAP PMIQYIPVPP PPPIGTVIPI QHIRSVTGEP PRN PREIPI WLGRNAPAID GVFPVTTPDL RCRIINAILG GNIGLSLTPG DCLTWDSAVA TLFIRTHGTF PMHQLGNVIK GIVD QEGVA TAYTLGMMLS GQNYQLVSGI IRGYLPGQAV VTALQQRLDQ EIDDQTRAET FIQHLNAVYE ILGLNARGQS IRASV TPQP RPSRGRGRGQ NTSRPSQGPA NSGRGRQRPA SGQSNRGSST QNQNQDNLNQ GGYNLRPRTY QPQRYGGGRG RRWNDN TNN QESRPSDQGS QTPRPNQAGS GVRGNQSQTP RPAAGRGGRG NHNRNQRSSG AGDSRAVNTV TQSATSSTDE SSSAVTA AS GGDQRD UniProtKB: Gag polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT |
---|---|
Output model | PDB-8ozn: |