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Open data
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Basic information
Entry | Database: PDB / ID: 6u7e | |||||||||
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Title | HCoV-229E RBD Class III in complex with human APN | |||||||||
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![]() | HYDROLASE/VIRAL PROTEIN / CoV / coronavirus / 229E / spike glycoprotein / APN / S-protein / HYDROLASE-VIRAL PROTEIN complex | |||||||||
Function / homology | ![]() membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / endoplasmic reticulum-Golgi intermediate compartment / : / Metabolism of Angiotensinogen to Angiotensins / aminopeptidase activity / secretory granule membrane / peptide binding / endocytosis involved in viral entry into host cell ...membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / endoplasmic reticulum-Golgi intermediate compartment / : / Metabolism of Angiotensinogen to Angiotensins / aminopeptidase activity / secretory granule membrane / peptide binding / endocytosis involved in viral entry into host cell / metallopeptidase activity / virus receptor activity / signaling receptor activity / angiogenesis / membrane => GO:0016020 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / cell differentiation / receptor-mediated virion attachment to host cell / external side of plasma membrane / fusion of virus membrane with host plasma membrane / lysosomal membrane / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / virion membrane / proteolysis / extracellular space / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tomlinson, A.C.A. / Li, Z. / Rini, J.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The human coronavirus HCoV-229E S-protein structure and receptor binding. Authors: Zhijie Li / Aidan Ca Tomlinson / Alan Hm Wong / Dongxia Zhou / Marc Desforges / Pierre J Talbot / Samir Benlekbir / John L Rubinstein / James M Rini / ![]() Abstract: The coronavirus S-protein mediates receptor binding and fusion of the viral and host cell membranes. In HCoV-229E, its receptor binding domain (RBD) shows extensive sequence variation but how S- ...The coronavirus S-protein mediates receptor binding and fusion of the viral and host cell membranes. In HCoV-229E, its receptor binding domain (RBD) shows extensive sequence variation but how S-protein function is maintained is not understood. Reported are the X-ray crystal structures of Class III-V RBDs in complex with human aminopeptidase N (hAPN), as well as the electron cryomicroscopy structure of the 229E S-protein. The structures show that common core interactions define the specificity for hAPN and that the peripheral RBD sequence variation is accommodated by loop plasticity. The results provide insight into immune evasion and the cross-species transmission of 229E and related coronaviruses. We also find that the 229E S-protein can expose a portion of its helical core to solvent. This is undoubtedly facilitated by hydrophilic subunit interfaces that we show are conserved among coronaviruses. These interfaces likely play a role in the S-protein conformational changes associated with membrane fusion. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 833.4 KB | Display | ![]() |
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PDB format | ![]() | 692 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6u7fC ![]() 6u7gC ![]() 6u7hC ![]() 4fyqS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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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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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 103522.031 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 66-967) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 15664.968 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 3 types, 16 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 7 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #7: 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: 3.07 Å3/Da / Density % sol: 59.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jan 21, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.99→48.092 Å / Num. obs: 58215 / % possible obs: 99.8 % / Redundancy: 3.642 % / Biso Wilson estimate: 81.905 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.083 / Χ2: 1.024 / Net I/σ(I): 11.06 / Num. measured all: 212045 / Scaling rejects: 12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4FYQ Resolution: 3→48.092 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.05 / 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: 227.29 Å2 / Biso mean: 97.7358 Å2 / Biso min: 46.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→48.092 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -24.614 Å / Origin y: -18.6671 Å / Origin z: -38.2449 Å
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Refinement TLS group |
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