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- PDB-8x7z: Crystal structure of CCoV-HuPn-2018 fusion core -

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Basic information

Entry
Database: PDB / ID: 8x7z
TitleCrystal structure of CCoV-HuPn-2018 fusion core
Components
  • HR1
  • HR2
KeywordsVIRAL PROTEIN / CCoV-HuPn-2018 / fusion core / postfusion
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
Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesCoronaviridae (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYan, L. / Yang, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Viruses / Year: 2024
Title: Crystal Structures of Fusion Cores from CCoV-HuPn-2018 and SADS-CoV.
Authors: Wang, F. / Yang, G. / Yan, L.
History
DepositionNov 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HR1
B: HR2


Theoretical massNumber of molelcules
Total (without water)14,9482
Polymers14,9482
Non-polymers00
Water2,108117
1
A: HR1
B: HR2

A: HR1
B: HR2

A: HR1
B: HR2


Theoretical massNumber of molelcules
Total (without water)44,8436
Polymers44,8436
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 area22950 Å2
ΔGint-226 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.615, 45.615, 428.683
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Components on special symmetry positions
IDModelComponents
11A-1222-

HOH

21A-1255-

HOH

31A-1263-

HOH

41B-1420-

HOH

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Components

#1: Protein HR1


Mass: 9044.052 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coronaviridae (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8E6CMP0
#2: Protein HR2


Mass: 5903.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coronaviridae (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: D2WXL7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M TRIS pH 8.5, 25% PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→71.45 Å / Num. obs: 10736 / % possible obs: 99.7 % / Redundancy: 1 % / Biso Wilson estimate: 10.87 Å2 / CC1/2: 0.8 / Net I/σ(I): 2
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 10736 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→71.45 Å / SU ML: 0.212 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3537
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.279 501 4.68 %
Rwork0.2506 10210 -
obs0.2519 10711 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.22 Å2
Refinement stepCycle: LAST / Resolution: 2.1→71.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 0 117 1162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411054
X-RAY DIFFRACTIONf_angle_d1.47411433
X-RAY DIFFRACTIONf_chiral_restr0.4009180
X-RAY DIFFRACTIONf_plane_restr0.0045188
X-RAY DIFFRACTIONf_dihedral_angle_d2.6626138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.310.34591220.28512498X-RAY DIFFRACTION100
2.31-2.650.29861170.26682505X-RAY DIFFRACTION100
2.65-3.330.28511330.23522525X-RAY DIFFRACTION100
3.33-71.450.2351290.23572682X-RAY DIFFRACTION98.91

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