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- PDB-1wnc: Crystal structure of the SARS-CoV Spike protein fusion core -

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Basic information

Entry
Database: PDB / ID: 1wnc
TitleCrystal structure of the SARS-CoV Spike protein fusion core
ComponentsE2 glycoprotein
KeywordsVIRAL PROTEIN / SARS-CoV / Spike protein / Fusion Core / Heptad repeat
Function / homology
Function and homology information


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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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, receptor-binding domain, SARS-CoV / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 speciesSARS coronavirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXu, Y. / Lou, Z. / Liu, Y. / Pang, H. / Tien, P. / Gao, G.F. / Rao, Z.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of severe acute respiratory syndrome coronavirus spike protein fusion core
Authors: Xu, Y. / Lou, Z. / Liu, Y. / Pang, H. / Tien, P. / Gao, G.F. / Rao, Z.
History
DepositionJul 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Nov 10, 2021Group: Database references / Category: 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

Downloads & links

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Assembly

Deposited unit
A: E2 glycoprotein
B: E2 glycoprotein
C: E2 glycoprotein
D: E2 glycoprotein
E: E2 glycoprotein
F: E2 glycoprotein


Theoretical massNumber of molelcules
Total (without water)71,3536
Polymers71,3536
Non-polymers00
Water11,728651
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: E2 glycoprotein
B: E2 glycoprotein
C: E2 glycoprotein


Theoretical massNumber of molelcules
Total (without water)35,6763
Polymers35,6763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-59 kcal/mol
Surface area12580 Å2
MethodPISA
3
D: E2 glycoprotein
E: E2 glycoprotein
F: E2 glycoprotein


Theoretical massNumber of molelcules
Total (without water)35,6763
Polymers35,6763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-57 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.215, 66.316, 69.976
Angle α, β, γ (deg.)90.00, 107.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
E2 glycoprotein / Spike glycoprotein / Peplomer protein


Mass: 11892.127 Da / Num. of mol.: 6 / Fragment: residues 900-1184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P59594
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 1.7 Å3/Da / Density % sol: 28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 2.5
Details: PEG4000, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 11974
Reflection shellResolution: 2.8→2.9 Å

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å
RfactorNum. reflection
Rfree0.273 552
Rwork0.233 -
obs0.233 10166
all-10715
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 0 651 4131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.8

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