+Open data
-Basic information
Entry | Database: PDB / ID: 7x72 | ||||||
---|---|---|---|---|---|---|---|
Title | SFTSV 5 fold pentamer | ||||||
Components | (Envelopment polyprotein) x 2 | ||||||
Keywords | VIRAL PROTEIN / SFTSV / virus / glycoproteins / assembly | ||||||
Function / homology | Function and homology information host cell Golgi membrane / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Severe fever with thrombocytopenia syndrome virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å | ||||||
Authors | Sun, Z. / Lou, Z. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Protein Cell / Year: 2023 Title: Architecture of severe fever with thrombocytopenia syndrome virus. Authors: Zixian Sun / Jing Cheng / Yuan Bai / Lin Cao / Daoxin Xie / Fei Deng / Xinzheng Zhang / Zihe Rao / Zhiyong Lou / | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7x72.cif.gz | 161.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7x72.ent.gz | 122.4 KB | Display | PDB format |
PDBx/mmJSON format | 7x72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x72_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7x72_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7x72_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 7x72_validation.cif.gz | 52.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/7x72 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/7x72 | HTTPS FTP |
-Related structure data
Related structure data | 33030MC 7x6uC 7x6wC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 5
2 |
|
3 |
|
Symmetry | Point symmetry: (Schoenflies symbol: C5 (5 fold cyclic)) |
-Components
#1: Protein | Mass: 61745.293 Da / Num. of mol.: 1 / Fragment: Gn / Source method: isolated from a natural source Source: (natural) Severe fever with thrombocytopenia syndrome virus Cell line: Vero / References: UniProt: A0A1S6XXI4 |
---|---|
#2: Protein | Mass: 54927.797 Da / Num. of mol.: 1 / Fragment: Gc / Source method: isolated from a natural source Source: (natural) Severe fever with thrombocytopenia syndrome virus Cell line: Vero / References: UniProt: A0A1S6XXK1 |
#3: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Severe fever with thrombocytopenia syndrome virus / Type: VIRUS / Entity ID: #1-#2 / Source: NATURAL |
---|---|
Source (natural) | Organism: Severe fever with thrombocytopenia syndrome virus / Strain: SFTSV- HBMC5_human_2016 |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 1.38 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Image processing |
| ||||||||||||||||||||||||
CTF correction |
| ||||||||||||||||||||||||
3D reconstruction | Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118467 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 7.2 Å | ||||||||||||||||||||||||
Refine LS restraints |
|