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- PDB-5zvm: Crystal Structure of the Human Coronavirus SARS HR1 motif in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zvm | ||||||
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Title | Crystal Structure of the Human Coronavirus SARS HR1 motif in complex with pan-CoVs inhibitor EK1 | ||||||
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![]() | VIRAL PROTEIN/INHIBITOR / SARS / Spike protein / S2 domain / HR1 motif / pan-Coronavirus / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | ![]() Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yan, L. / Yang, B. / Wilson, I.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike. Authors: Xia, S. / Yan, L. / Xu, W. / Agrawal, A.S. / Algaissi, A. / Tseng, C.K. / Wang, Q. / Du, L. / Tan, W. / Wilson, I.A. / Jiang, S. / Yang, B. / Lu, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.7 KB | Display | ![]() |
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PDB format | ![]() | 55 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.9 KB | Display | ![]() |
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Full document | ![]() | 465.4 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zuvC ![]() 5zvkC ![]() 2bezS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: 8698.673 Da / Num. of mol.: 3 / Fragment: UNP residues 892-970 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 4923.550 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: The manually designed EK1 inhibitor was modified from a Coronavirus sequence (UNP P36334 SPIKE_CVHOC, UNP residues 880-916). Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() Sequence details | THE PROTEIN USED FOR CRYSTALLIZATION IS A HR1-SGGRGG-EK1 FUSION PROTEIN THAT CONTAINS SARS HR1 ...THE PROTEIN USED FOR CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.61 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 5.5 / Details: 0.2M Li2SO4, 0.1M BIS-Tris, pH 5.5, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→34.5 Å / Num. obs: 6070 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 97.8 Å2 / Rpim(I) all: 0.06 / Rrim(I) all: 0.172 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 595 / CC1/2: 0.74 / Rpim(I) all: 0.363 / Rrim(I) all: 1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2bez Resolution: 3.3→34.5 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.823 / SU B: 31.889 / SU ML: 0.521 / Cross valid method: THROUGHOUT / ESU R Free: 0.689
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 112 Å2
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Refinement step | Cycle: 1 / Resolution: 3.3→34.5 Å
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Refine LS restraints |
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