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Yorodumi- PDB-7q3r: Crystal structure of SARS-CoV-2 RBD in complex with the neutraliz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q3r | ||||||
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Title | Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobodies VHH-F04 and VHH-G09 | ||||||
Components |
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Keywords | VIRAL PROTEIN / Coronavirus / nanobody | ||||||
Function / homology | Function and homology information endocytosis involved in viral entry into host cell / membrane => GO:0016020 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Fernandez, I. / Pederzoli, R. / Rey, F.A. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: NANOBODIES AGAINST SARS-COV-2 NEUTRALIZE VARIANTS OF CONCERN AND EXPLORE CONFORMATIONAL DIFFERENCES ON THE SPIKE PROTEIN Authors: Fernandez, I. / Rey, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q3r.cif.gz | 198.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q3r.ent.gz | 155.9 KB | Display | PDB format |
PDBx/mmJSON format | 7q3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q3r_validation.pdf.gz | 802.6 KB | Display | wwPDB validaton report |
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Full document | 7q3r_full_validation.pdf.gz | 804.6 KB | Display | |
Data in XML | 7q3r_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 7q3r_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/7q3r ftp://data.pdbj.org/pub/pdb/validation_reports/q3/7q3r | HTTPS FTP |
-Related structure data
Related structure data | 7q3qC 6ym0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules FG
#2: Antibody | Mass: 15465.069 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 14776.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human) |
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 22277.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Homo sapiens (human) / References: UniProt: A0A6H2EIN2 |
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#4: 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 |
-Non-polymers , 2 types, 282 molecules
#5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M NaAc/HAc (pH 4.5), 0.2 M Li2SO4, 2.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978565 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 30, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978565 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.92→48.03 Å / Num. obs: 69234 / % possible obs: 99.8 % / Redundancy: 20.7 % / Biso Wilson estimate: 40.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.018 / Rrim(I) all: 0.081 / Net I/σ(I): 22.5 / Num. measured all: 1433441 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YM0 Resolution: 1.92→45.91 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.36 / 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: 102.18 Å2 / Biso mean: 46.6338 Å2 / Biso min: 25.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.92→45.91 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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Refinement TLS params. | Method: refined / Origin x: 57.0235 Å / Origin y: 56.8455 Å / Origin z: 18.1546 Å
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Refinement TLS group |
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