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- PDB-8xlm: Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8xlm | |||||||||||||||||||||
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Title | Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein in complex with ACE2 (1-up state) | |||||||||||||||||||||
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Function / homology | ![]() positive regulation of amino acid transport / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Nomai, T. / Anraku, Y. / Kita, S. / Hashiguchi, T. / Maenaka, K. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant Authors: Nomai, T. / Anraku, Y. / Kita, S. / Hashiguchi, T. / Maenaka, K. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 729.3 KB | Display | ![]() |
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PDB format | ![]() | 584.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 38453MC ![]() 8wmdC ![]() 8wmfC ![]() 8xlnC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | ![]() Mass: 138062.094 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 / Cell line (production host): HEK293 / Production host: ![]() ![]() #2: Protein | | Mass: 70485.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 4 types, 43 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 / ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 / Details: calcium- and magnesium-free PBS buffer. | ||||||||||||||||||||||||
Specimen | 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. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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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: 51.837 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 5381 |
EM imaging optics | Energyfilter name![]() |
Image scans | Width: 5760 / Height: 4092 |
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Processing
EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3967269 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57561 / 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 |
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