[English] 日本語
![](img/lk-miru.gif)
- PDB-8jyn: Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex wit... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8jyn | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (1-up state) | ||||||||||||||||||
![]() |
| ||||||||||||||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Function / homology | ![]() positive regulation of amino acid transport / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Yajima, H. / Anraku, Y. / Kita, S. / Kimura, K. / Sasaki, J. / Sasaki-Tabata, K. / Maenaka, K. / Hashiguchi, T. | ||||||||||||||||||
Funding support | ![]()
| ||||||||||||||||||
![]() | ![]() Title: Virological characteristics of the SARS-CoV-2 XBB.1.5 variant Authors: Tamura, T. / Ito, J. / Uriu, K. / Zahradnik, J. / Kida, I. / Anraku, Y. / Nasser, H. / Shofa, M. / Oda, Y. / Lytras, S. / Nao, N. / Itakura, Y. / Deguchi, S. / Suzuki, R. / Wang, L. / Begum, ...Authors: Tamura, T. / Ito, J. / Uriu, K. / Zahradnik, J. / Kida, I. / Anraku, Y. / Nasser, H. / Shofa, M. / Oda, Y. / Lytras, S. / Nao, N. / Itakura, Y. / Deguchi, S. / Suzuki, R. / Wang, L. / Begum, M.M. / Kita, S. / Yajima, H. / Sasaki, J. / Sasaki-Tabata, K. / Shimizu, R. / Tsuda, M. / Kosugi, Y. / Fujita, S. / Pan, L. / Sauter, D. / Yoshimatsu, K. / Suzuki, S. / Asakura, H. / Nagashima, M. / Sadamasu, K. / Yoshimura, K. / Yamamoto, Y. / Nagamoto, T. / Schreiber, G. / Maenaka, K. / Hashiguchi, T. / Ikeda, T. / Fukuhara, T. / Saito, A. / Tanaka, S. / Matsuno, K. / Takayama, K. / Sato, K. | ||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 764.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 608.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 36727MC ![]() 8jykC ![]() 8jymC ![]() 8jyoC ![]() 8jypC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | ![]() Mass: 138086.094 Da / Num. of mol.: 3 Mutation: F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2 / Production host: ![]() ![]() #2: Protein | | Mass: 70485.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Sugars , 4 types, 45 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ![]() Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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 #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-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 #6: Sugar | ChemComp-NAG / ![]() |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
-
Sample preparation
Component | Name: SARS-CoV-2 XBB1.5 spike glycoprotein with ACE2 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K / Details: blotting time 5 s and blotting force 5. |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 50.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7474 |
EM imaging optics | Energyfilter name![]() |
Image scans | Width: 5760 / Height: 4092 |
-
Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1831441 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58221 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8IOU Accession code: 8IOU / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|