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- PDB-7owx: Structure of coiled-coil tetramer from SARS-CoV-2 spike stalk region -

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Basic information

Entry
Database: PDB / ID: 7owx
TitleStructure of coiled-coil tetramer from SARS-CoV-2 spike stalk region
ComponentsSpike protein S2
KeywordsVIRAL PROTEIN / spike / sars-cov-2 / coiled-coil / tetramer / virus / coronavirus
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.929 Å
AuthorsZivic, Z. / Hadzi, S.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyJ1-1706 Slovenia
Slovenian Research AgencyP1-0201 Slovenia
CitationJournal: Faseb J. / Year: 2022
Title: Structural polymorphism of coiled-coils from the stalk domain of SARS-CoV-2 spike protein.
Authors: Zivic, Z. / Strmsek, Z. / Novinec, M. / Lah, J. / Hadzi, S.
History
DepositionJun 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S2
B: Spike protein S2
C: Spike protein S2
D: Spike protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1919
Polymers12,8744
Non-polymers3175
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, tetramer in crystal, trimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-67 kcal/mol
Surface area6410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.140, 45.540, 47.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
Spike protein S2


Mass: 3218.591 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.92 Å3/Da / Density % sol: 35.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.002 M zinc chloride, 0.1 M Tris pH 8, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.929→32.85 Å / Num. obs: 7780 / % possible obs: 99.3 % / Redundancy: 10.8 % / Biso Wilson estimate: 26.97 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.15 / Net I/σ(I): 11.5
Reflection shellResolution: 1.929→2.0495 Å / Redundancy: 18.1 % / Num. unique obs: 729 / CC1/2: 0.68 / Rrim(I) all: 1.43 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.929→32.85 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 777 9.99 %
Rwork0.1718 7004 -
obs0.1779 7779 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.64 Å2 / Biso mean: 37.6203 Å2 / Biso min: 19.73 Å2
Refinement stepCycle: final / Resolution: 1.929→32.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 14 76 970
Biso mean--41.94 46.11 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006923
X-RAY DIFFRACTIONf_angle_d0.731238
X-RAY DIFFRACTIONf_chiral_restr0.041148
X-RAY DIFFRACTIONf_plane_restr0.004167
X-RAY DIFFRACTIONf_dihedral_angle_d7.623704
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.929-2.04950.34591240.247372895
2.0495-2.20770.27671280.19641151100
2.2077-2.42980.2451350.16651151100
2.4298-2.78130.22321240.16041172100
2.7813-3.50350.21641360.16591188100
3.5035-33.0040.22081300.16681252100
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)
10.09340.0179-0.03530.0035-0.0070.01290.0361-0.01490.17990.10780.09880.24890.0606-0.07160.00310.25390.00390.00820.2381-0.00050.290328.7598-10.779220.5373
20.09010.03150.10750.06780.0620.1387-0.14570.19530.1741-0.01240.27330.30660.1116-0.37290.00040.2991-0.0191-0.03240.3271-0.03130.303429.1243-15.265812.0883
30.13260.0232-0.03390.05350.05620.08590.0133-0.022-0.0188-0.1485-0.0755-0.05350.01930.014200.26230.00440.01950.2361-0.0240.243839.2877-14.720812.6497
40.2228-0.0465-0.02660.01810.0570.32160.0336-0.1072-0.00460.2083-0.1195-0.20230.04020.0471-0.00010.23770.01560.02170.25630.01010.262238.6409-14.128821.7977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1177 through 1203)A1177 - 1203
2X-RAY DIFFRACTION2(chain 'B' and resid 1177 through 1203)B1177 - 1203
3X-RAY DIFFRACTION3(chain 'C' and resid 1177 through 1203)C1177 - 1203
4X-RAY DIFFRACTION4(chain 'D' and resid 1177 through 1203)D1177 - 1203

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