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- PDB-7p8j: Receptor-binding domain (RBD) of the spike protein of the bat cor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p8j | ||||||||||||||||||||||||
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Title | Receptor-binding domain (RBD) of the spike protein of the bat coronavirus RaTG13 virus in complex with the extracellular domain of human angiotensin-converting enzyme 2 (ACE2) - Crystal form 2 | ||||||||||||||||||||||||
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![]() | CELL INVASION / COVID-19 / Bat coronavirus / Spillover / Zoonotic viral infection / Evolution | ||||||||||||||||||||||||
Function / homology | ![]() positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / Attachment and Entry / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / endocytosis involved in viral entry into host cell / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / endocytic vesicle membrane / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / cell surface / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Scietti, L. / Castelli, M. / Faravelli, S. / Clementi, N. / Mancini, N. / Forneris, F. | ||||||||||||||||||||||||
Funding support | ![]() ![]() ![]() ![]() ![]()
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![]() | ![]() Title: Constrained Evolution of SARS-CoV-2 Spike in Rhinolophus affinis Bats Authors: Castelli, M. / Scietti, L. / Faravelli, S. / Clementi, N. / Forneris, F. / Mancini, N. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 298 KB | Display | ![]() |
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PDB format | ![]() | 228.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 34.2 KB | Display | |
Data in CIF | ![]() | 51.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vw1S S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 69511.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Initial GS and final AAA sequences were introduced by molecular cloning Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 26265.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: cloning artifacts: GS sequence at the N-terminus and AA sequence at the C-terminus, + 6xHis-tag at the C-terminus Source: (gene. exp.) ![]() ![]() #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 Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.9 Details: 0.2-0.25 M sodium thiocyanate, 18-23% PEG 3350, pH 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 6.5→66.42 Å / Num. obs: 5280 / % possible obs: 99.7 % / Redundancy: 8.5 % / CC1/2: 0.979 / Rmerge(I) obs: 0.459 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 6.5→7.26 Å / Redundancy: 8.9 % / Rmerge(I) obs: 2.905 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1424 / CC1/2: 0.531 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6VW1 Resolution: 6.585→49.516 Å / SU ML: 0.89 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 30 Å2 / Biso mean: 30 Å2 / Biso min: 30 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 6.585→49.516 Å
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 6.5855→49.516 Å / Rfactor Rfree error: 0
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