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- PDB-8cwj: Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin rece... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cwj | ||||||
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Title | Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain (pRBD) | ||||||
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![]() | IMMUNE SYSTEM / antibody / pangolin / receptor binding domain / class 5 epitope | ||||||
Function / homology | ![]() endocytosis involved in viral entry into host cell / 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 / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Langley, D.B. / Christ, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Neutralization of CoV-2 omicron lineages by affinity-matured class 5 antibodies Authors: Langley, D.B. / Christ, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 843 KB | Display | ![]() |
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PDB format | ![]() | 700.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8cwiC 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules GI
#3: Protein | Mass: 22891.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Antibody , 4 types, 8 molecules HALBJUKV
#1: Antibody | Mass: 24428.432 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 24289.885 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Antibody | Mass: 24514.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Antibody | Mass: 23466.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 388 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-GOL / #9: Chemical | ChemComp-CL / #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.32 % / Description: tiles |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Equal volumes of protein complex (1:1:1 molar ratio, at ~ 5 mg/mL, in 25 mM Tris (pH 8.0), 200 mM NaCl) were combined with well solution (200 mM sodium citrate (pH 5.6), 12% (w/v) PEG6000). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9536 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.449→48.69 Å / Num. obs: 122620 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 55.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.044 / Rrim(I) all: 0.119 / Net I/σ(I): 11.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: generic RBD and Fab Resolution: 2.449→48.69 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.03 / 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: 168.95 Å2 / Biso mean: 70.3295 Å2 / Biso min: 28.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.449→48.69 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 41.9371 Å / Origin y: 2.277 Å / Origin z: 39.4967 Å
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Refinement TLS group |
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