[English] 日本語
![](img/lk-miru.gif)
- EMDB-10813: In-situ structure of a dimer of the trimeric HEF from influenza C... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-10813 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | In-situ structure of a dimer of the trimeric HEF from influenza C viral particles without a matrix layer by cryo-ET | ||||||||||||
![]() | Post-processed map. Dimer of trimers from virions without a matrix layer | ||||||||||||
![]() |
| ||||||||||||
Function / homology | ![]() sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | subtomogram averaging / ![]() | ||||||||||||
![]() | Halldorsson S / Rosenthal PB | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: In situ structure and organization of the influenza C virus surface glycoprotein. Authors: Steinar Halldorsson / Kasim Sader / Jack Turner / Lesley J Calder / Peter B Rosenthal / ![]() ![]() Abstract: The lipid-enveloped influenza C virus contains a single surface glycoprotein, the haemagglutinin-esterase-fusion (HEF) protein, that mediates receptor binding, receptor destruction, and membrane ...The lipid-enveloped influenza C virus contains a single surface glycoprotein, the haemagglutinin-esterase-fusion (HEF) protein, that mediates receptor binding, receptor destruction, and membrane fusion at the low pH of the endosome. Here we apply electron cryotomography and subtomogram averaging to describe the structural basis for hexagonal lattice formation by HEF on the viral surface. The conformation of the glycoprotein in situ is distinct from the structure of the isolated trimeric ectodomain, showing that a splaying of the membrane distal domains is required to mediate contacts that form the lattice. The splaying of these domains is also coupled to changes in the structure of the stem region which is involved in membrane fusion, thereby linking HEF's membrane fusion conformation with its assembly on the virus surface. The glycoprotein lattice can form independent of other virion components but we show a major role for the matrix layer in particle formation. | ||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 28.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 20.7 KB 20.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.2 KB | Display | ![]() |
Images | ![]() | 133.3 KB | ||
Masks | ![]() | 30.5 MB | ![]() | |
Others | ![]() ![]() ![]() | 22.4 MB 22.5 MB 22.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Post-processed map. Dimer of trimers from virions without a matrix layer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unfiltered map
File | emd_10813_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unfiltered map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 1
File | emd_10813_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2
File | emd_10813_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Influenza C virus
Entire | Name: ![]() ![]() |
---|---|
Components |
|
-Supramolecule #1: Influenza C virus
Supramolecule | Name: Influenza C virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified from infected cells. / NCBI-ID: 11552 / Sci species name: Influenza C virus / Sci species strain: C/Johannesburg/1/1966 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
---|---|
Host (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Hemagglutinin esterase fusion
Macromolecule | Name: Hemagglutinin esterase fusion / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: ![]() |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Sequence | String: MFFSLLLVLG LTEAEKIKIC LQKQVNSSFS LHNGFGGNLY ATEEKRMFEL VKPKAGASVL NQSTWIGFG DSRTDKSNSA FPRSADVSAK TADKFRFLSG GSLMLSMFGP PGKVDYLYQG C GKHKVFYE GVNWSPHAAI NCYRKNWTDI KLNFQKNIYE LASQSHCMSL ...String: MFFSLLLVLG LTEAEKIKIC LQKQVNSSFS LHNGFGGNLY ATEEKRMFEL VKPKAGASVL NQSTWIGFG DSRTDKSNSA FPRSADVSAK TADKFRFLSG GSLMLSMFGP PGKVDYLYQG C GKHKVFYE GVNWSPHAAI NCYRKNWTDI KLNFQKNIYE LASQSHCMSL VNALDKTIPL QV TAGTAGN CNNSFLKNPA LYTQEVKPSE NKCGKENLAF FTLPTQFGTY ECKLHLVASC YFI YDSKEV YNKRGCDNYF QVIYDSFGKV VGGLDNRVSP YTGNSGDTPT MQCDMLQLKP GRYS VRSSP RFLLMPERSY CFDMKEKGPV TAVQSIWGKG RESDYAVDQA CLSTPGCMLI QKQKP YIGE ADDHHGDQEM RELLSGLDYE ARCISQSGWV NETSPFTEKY LLPPKFGRCP LAAKEE SIP KIPDGLLIPT SGTDTTVTKP KSRIFGIDDL IIGVLFVAIV ETGIGGYLLG SRKESGG GV TKESAEKGFE KIGNDIQILK SSINIAIEKL NDRISHDEQA IRDLTLEIEN ARSEALLG E LGIIRALLVG NISIGLQESL WELASEITNR AGDLAVEVSP GCWIIDNNIC DQSCQNFIF KFNETAPVPT IPPLDTKIDL QSDPFYWGSS LGLAITATIS LAALVISGIA ICRTK |
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | subtomogram averaging |
Aggregation state | particle |
-
Sample preparation
Concentration | 2 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.4 Component:
| ||||||||||||
Grid | Model: Quantifoil / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III | ||||||||||||
Details | Heterogeneous mix of viral particles, viral like particles and cellular vesicles |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 2 / Average exposure time: 1.57 sec. / Average electron dose: 1.57 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
---|---|
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |