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- PDB-1zva: A structure-based mechanism of SARS virus membrane fusion -

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Basic information

Entry
Database: PDB / ID: 1zva
TitleA structure-based mechanism of SARS virus membrane fusion
ComponentsE2 glycoprotein
KeywordsVIRAL PROTEIN / SARS coronavirus / membrane fusion / S2 / virus entry / coiled coils / conformational change
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDeng, Y. / Liu, J. / Zheng, Q. / Yong, W. / Dai, J. / Lu, M.
CitationJournal: Structure / Year: 2006
Title: Structures and Polymorphic Interactions of Two Heptad-Repeat Regions of the SARS Virus S2 Protein.
Authors: Deng, Y. / Liu, J. / Zheng, Q. / Yong, W. / Lu, M.
History
DepositionJun 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Aug 23, 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
Remark 999SEQUENCE In comparison with the protein database sequence, residues 963-1149 have been deleted in ...SEQUENCE In comparison with the protein database sequence, residues 963-1149 have been deleted in the current entry and replaced with a linker sequence comprising of residues 38-43 (SGGRGG).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E2 glycoprotein


Theoretical massNumber of molelcules
Total (without water)8,1101
Polymers8,1101
Non-polymers00
Water1,36976
1
A: E2 glycoprotein

A: E2 glycoprotein


Theoretical massNumber of molelcules
Total (without water)16,2202
Polymers16,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2930 Å2
ΔGint-36 kcal/mol
Surface area8370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.970, 146.593, 24.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a dimer of hairpins, i.e. four-helix bundle

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Components

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


Mass: 8110.027 Da / Num. of mol.: 1 / Fragment: residues 926-962 and residues 1150-1183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Strain: SARS / Gene: S / Plasmid: pN37/C34 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/pLysis / References: UniProt: P59594
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.1 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 1500, sodium formate, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0358
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 3, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0358 Å / Relative weight: 1
ReflectionResolution: 1.5→72.6 Å / Num. obs: 11906 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 7.1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZV7

1zv7


Resolution: 1.5→72.55 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.293 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.246 563 4.7 %RANDOM
Rwork0.211 ---
obs0.213 11904 98 %-
all-11904 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.5→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms551 0 0 76 627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.962743
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.454574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02405
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.2243
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9191.5367
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8382585
X-RAY DIFFRACTIONr_scbond_it3.0373184
X-RAY DIFFRACTIONr_scangle_it4.8214.5158
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.221 41
Rwork0.241 803
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8606-0.4348-0.47285.2288-0.39711.20930.0504-0.17580.1541-0.06390.1310.0749-0.27680.1164-0.18140.1234-0.04130.01540.0599-0.03220.097718.15449.84210.531
21.14921.6422-0.790911.4883-3.47642.4089-0.01870.00420.0792-0.17530.05010.143-0.1257-0.0074-0.03140.0263-0.0037-0.01250.015-0.00120.036414.25147.6653.571
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 371 - 37
2X-RAY DIFFRACTION2AA44 - 7544 - 75

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