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- PDB-1wdg: crystal structure of MHV spike protein fusion core -

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Basic information

Entry
Database: PDB / ID: 1wdg
Titlecrystal structure of MHV spike protein fusion core
ComponentsE2 glycoprotein
KeywordsVIRAL PROTEIN / MHV / coronavirus / heptad repeat / fusion core / viral entry
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell Golgi apparatus / 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 / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMurine hepatitis virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsXu, Y. / Liu, Y. / Lou, Z. / Qin, L. / Li, X. / Bai, Z. / Tien, P. / Gao, G.F. / Rao, Z.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Basis for Coronavirus-mediated Membrane Fusion: CRYSTAL STRUCTURE OF MOUSE HEPATITIS VIRUS SPIKE PROTEIN FUSION CORE
Authors: Xu, Y. / Liu, Y. / Lou, Z. / Qin, L. / Li, X. / Bai, Z. / Pang, H. / Tien, P. / Gao, G.F. / Rao, Z.
History
DepositionMay 14, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Aug 23, 2017Group: Data collection / Category: reflns / Item: _reflns.number_obs
Revision 1.5Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E2 glycoprotein
B: E2 glycoprotein


Theoretical massNumber of molelcules
Total (without water)19,7742
Polymers19,7742
Non-polymers00
Water6,359353
1
A: E2 glycoprotein
B: E2 glycoprotein

A: E2 glycoprotein
B: E2 glycoprotein

A: E2 glycoprotein
B: E2 glycoprotein


Theoretical massNumber of molelcules
Total (without water)59,3226
Polymers59,3226
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_635-y+1,x-y-2,z1
crystal symmetry operation3_865-x+y+3,-x+1,z1
2
B: E2 glycoprotein

B: E2 glycoprotein

B: E2 glycoprotein


Theoretical massNumber of molelcules
Total (without water)29,6613
Polymers29,6613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_635-y+1,x-y-2,z1
crystal symmetry operation3_865-x+y+3,-x+1,z1
Buried area6510 Å2
ΔGint-70 kcal/mol
Surface area11370 Å2
MethodPISA, PQS
3
A: E2 glycoprotein

A: E2 glycoprotein

A: E2 glycoprotein


Theoretical massNumber of molelcules
Total (without water)29,6613
Polymers29,6613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.6, 51.6, 198.2
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Detailsthree molecules in one biological unit and two molecules in one asymmetric unit

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Components

#1: Protein E2 glycoprotein / MHV spike protein


Mass: 9887.039 Da / Num. of mol.: 2 / Fragment: nMHV 2-Helix
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine hepatitis virus / Genus: Coronavirus / Strain: A59 / Production host: Escherichia coli (E. coli) / References: UniProt: P11224
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 12068 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.06→2.13 Å

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→50 Å / σ(F): 0
RfactorNum. reflection
Rfree0.298 597
Rwork0.26 -
all0.269 12194
obs0.262 11689
Refinement stepCycle: LAST / Resolution: 2.06→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 0 353 1543
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.012

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