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- PDB-5yl9: 1.86 Angstrom crystal structure of human Coronavirus 229E fusion core -

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Basic information

Entry
Database: PDB / ID: 5yl9
Title1.86 Angstrom crystal structure of human Coronavirus 229E fusion core
Components(Spike glycoproteinSpike protein) x 2
KeywordsVIRAL PROTEIN / Spike protein / 6-helical bundle / post-fusion state
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: 1.861 Å
AuthorsYang, B. / Yan, L. / Meng, B. / WIlson, I.A.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31600619 China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Crystal structure of the post-fusion core of the Human coronavirus 229E spike protein at 1.86 angstrom resolution
Authors: Yan, L. / Meng, B. / Xiang, J. / Wilson, I.A. / Yang, B.
History
DepositionOct 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 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
B: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)16,2532
Polymers16,2532
Non-polymers00
Water2,072115
1
A: Spike glycoprotein
B: Spike glycoprotein

A: Spike glycoprotein
B: Spike glycoprotein

A: Spike glycoprotein
B: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)48,7596
Polymers48,7596
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area24540 Å2
ΔGint-215 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.941, 46.941, 402.145
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-911-

HOH

21A-928-

HOH

31A-936-

HOH

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Components

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


Mass: 9713.730 Da / Num. of mol.: 1 / Fragment: UNP residues 785-872
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Gene: S / Production host: Escherichia coli (E. coli) / References: UniProt: P15423
#2: Protein Spike glycoprotein / Spike protein / S glycoprotein


Mass: 6539.273 Da / Num. of mol.: 1 / Fragment: UNP residues 1052-1104
Source method: isolated from a genetically manipulated source
Details: HCoV-229E spike protein resi 1052-1105 fused to a N-termnal SGGRGG linker
Source: (gene. exp.) Human coronavirus 229E / Gene: S / Production host: Escherichia coli (E. coli) / References: UniProt: P15423
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe fusion protein (HR1-SGGRGG-HR2) was cleaved before the crystallization. As for the chain A (HR1) ...The fusion protein (HR1-SGGRGG-HR2) was cleaved before the crystallization. As for the chain A (HR1), a part of the N-terminal affinity tag "SER" was included in the crystal, but not visible. As for the chian B (HR2), the linker residues 'RGG' were visible in the density map.

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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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 293 K / Method: evaporation / Details: citric acid, BIS-TRIS propane, PEG3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.86→44.7 Å / Num. obs: 15101 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 24 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.016 / Rrim(I) all: 0.075 / Net I/σ(I): 31.5
Reflection shellResolution: 1.86→1.93 Å / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 1079 / CC1/2: 0.964 / Rpim(I) all: 0.143 / Rrim(I) all: 0.67 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IEQ

2ieq


Resolution: 1.861→44.683 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.32
RfactorNum. reflection% reflection
Rfree0.2065 764 5.06 %
Rwork0.1823 --
obs0.1836 14995 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.861→44.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 0 115 1224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061138
X-RAY DIFFRACTIONf_angle_d0.6321551
X-RAY DIFFRACTIONf_dihedral_angle_d13.734702
X-RAY DIFFRACTIONf_chiral_restr0.046196
X-RAY DIFFRACTIONf_plane_restr0.003202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8614-2.00510.26021580.1952784X-RAY DIFFRACTION100
2.0051-2.20690.17911420.16662813X-RAY DIFFRACTION100
2.2069-2.52620.19791350.16182850X-RAY DIFFRACTION100
2.5262-3.18270.19441630.18352862X-RAY DIFFRACTION100
3.1827-44.69560.21361660.19123022X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -19.0082 Å / Origin y: 14.4391 Å / Origin z: 8.3423 Å
111213212223313233
T0.0636 Å2-0.0023 Å2-0.0044 Å2-0.0702 Å20.0019 Å2--0.1885 Å2
L0.5414 °20.0135 °2-0.0845 °2-0.5213 °2-0.0135 °2--4.6773 °2
S-0.0633 Å °-0.0012 Å °-0.0214 Å °0.0145 Å °-0.0502 Å °-0.0528 Å °-0.0861 Å °0.1509 Å °0.1199 Å °
Refinement TLS groupSelection details: all

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