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- PDB-5zhy: Structural characterization of the HCoV-229E fusion core -

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Basic information

Entry
Database: PDB / ID: 5zhy
TitleStructural characterization of the HCoV-229E fusion core
ComponentsSpike glycoprotein, Spike glycoproteinSpike protein
KeywordsVIRAL PROTEIN / membrane fusion / broad-spectrum inhibitor design
Function / homology
Function and homology information


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 / virion membrane / membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesHuman coronavirus 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.441 Å
AuthorsZhang, W. / Zheng, Q. / Yan, M. / Chen, X. / Yang, H. / Zhou, W. / Rao, Z.
Funding support China, 5items
OrganizationGrant numberCountry
National Key R&D Program of China2017YFC0840300 China
MOST 973 ProjectNo. 2014CB542800 China
MOST 973 ProjectNo. 2014CBA02003 China
CAS SPR program BXDB08020200 China
National Science Foundation of China81330036 and 81520108019 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural characterization of the HCoV-229E fusion core.
Authors: Zhang, W. / Zheng, Q. / Yan, M. / Chen, X. / Yang, H. / Zhou, W. / Rao, Z.
History
DepositionMar 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike glycoprotein, Spike glycoprotein
B: Spike glycoprotein, Spike glycoprotein
C: Spike glycoprotein, Spike glycoprotein
D: Spike glycoprotein, Spike glycoprotein
E: Spike glycoprotein, Spike glycoprotein
F: Spike glycoprotein, Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)97,3686
Polymers97,3686
Non-polymers00
Water0
1
A: Spike glycoprotein, Spike glycoprotein
B: Spike glycoprotein, Spike glycoprotein
C: Spike glycoprotein, Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)48,6843
Polymers48,6843
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-76 kcal/mol
Surface area11880 Å2
MethodPISA
2
D: Spike glycoprotein, Spike glycoprotein
E: Spike glycoprotein, Spike glycoprotein
F: Spike glycoprotein, Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)48,6843
Polymers48,6843
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-74 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.108, 77.348, 77.386
Angle α, β, γ (deg.)76.89, 89.78, 90.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Spike glycoprotein, Spike glycoprotein / Spike protein


Mass: 16227.998 Da / Num. of mol.: 6 / Fragment: UNP residues 789-856. UNP residues 1053-1105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15423

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5 M Ammonium sulfate, 12% (v/v) Glycerol, 100 mM Tris/HCl, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 24629 / % possible obs: 97.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 17.2
Reflection shellResolution: 2.44→2.49 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1186 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IEQ

2ieq


Resolution: 2.441→31.006 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 2018 8.23 %
Rwork0.2243 --
obs0.2277 24511 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.441→31.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 0 0 4039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094046
X-RAY DIFFRACTIONf_angle_d1.0475500
X-RAY DIFFRACTIONf_dihedral_angle_d15.1761448
X-RAY DIFFRACTIONf_chiral_restr0.049741
X-RAY DIFFRACTIONf_plane_restr0.006700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4406-2.50160.41441340.32731505X-RAY DIFFRACTION89
2.5016-2.56920.4161370.28921562X-RAY DIFFRACTION97
2.5692-2.64480.3081460.26851629X-RAY DIFFRACTION98
2.6448-2.73010.2851530.25061621X-RAY DIFFRACTION97
2.7301-2.82760.31761310.24821586X-RAY DIFFRACTION97
2.8276-2.94070.29711470.24991627X-RAY DIFFRACTION97
2.9407-3.07450.29161440.25291651X-RAY DIFFRACTION98
3.0745-3.23640.33191510.22491557X-RAY DIFFRACTION97
3.2364-3.43890.26381470.22231635X-RAY DIFFRACTION98
3.4389-3.7040.22491470.20441626X-RAY DIFFRACTION98
3.704-4.07610.2571510.19651638X-RAY DIFFRACTION99
4.0761-4.66420.2161480.17681611X-RAY DIFFRACTION99
4.6642-5.86980.23211450.23991661X-RAY DIFFRACTION99
5.8698-31.00890.25881370.23151584X-RAY DIFFRACTION96

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