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- PDB-7cot: Structure of post fusion core of SARS-CoV-2 S2 subunit -

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Basic information

Entry
Database: PDB / ID: 7cot
TitleStructure of post fusion core of SARS-CoV-2 S2 subunit
ComponentsSpike glycoprotein
KeywordsVIRAL PROTEIN / COVID-19 / SARS-CoV-2 / Spike protein / Heptad repeat / Membrane fusion / Post fusion core
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 / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsLin, M.H. / Tan, K.P. / Hsu, C.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2628-B-002-013 Taiwan
Ministry of Science and Technology (MoST, Taiwan)108-2113-M-002-011 Taiwan
CitationJournal: To Be Published
Title: Crystal structure of post fusion core of SARS-CoV-2 S2 subunit
Authors: Tan, K.P. / Lin, M.H. / Kuo, P.C. / Hsu, C.H.
History
DepositionAug 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)41,5963
Polymers41,5963
Non-polymers00
Water1,72996
1
A: Spike glycoprotein

A: Spike glycoprotein

A: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)41,5963
Polymers41,5963
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11410 Å2
ΔGint-97 kcal/mol
Surface area15840 Å2
MethodPISA
2
B: Spike glycoprotein

B: Spike glycoprotein

B: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)41,5963
Polymers41,5963
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11510 Å2
ΔGint-98 kcal/mol
Surface area15770 Å2
MethodPISA
3
C: Spike glycoprotein

C: Spike glycoprotein

C: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)41,5963
Polymers41,5963
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10600 Å2
ΔGint-86 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.968, 51.968, 116.225
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
Components on special symmetry positions
IDModelComponents
11A-244-

HOH

21A-245-

HOH

31B-244-

HOH

41B-245-

HOH

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Components

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


Mass: 13865.412 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: post fusion core of SARS-CoV-2 S2 subunit
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.39 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 3350, 0.07M Bis-Tris propane pH 8.5, 0.03M citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: May 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.48
ReflectionResolution: 2.16→30 Å / Num. obs: 18634 / % possible obs: 98.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 22.22 Å2 / CC1/2: 0.8396 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.55
Reflection shellResolution: 2.16→2.2 Å / Rmerge(I) obs: 0.51 / Num. unique obs: 890 / CC1/2: 0.568

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WYY

1wyy


Resolution: 2.16→29.36 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 1772 9.94 %
Rwork0.1967 16060 -
obs0.2017 17832 93.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.41 Å2 / Biso mean: 55.3437 Å2 / Biso min: 7.55 Å2
Refinement stepCycle: final / Resolution: 2.16→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 0 96 2684
Biso mean---46.49 -
Num. residues----341
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.210.251040.2183991109578
2.21-2.280.26081390.21261129126883
2.28-2.350.27831230.19561175129889
2.35-2.440.2581240.18871170129491
2.44-2.530.24271350.18131261139695
2.53-2.650.23531560.19061278143497
2.65-2.790.25551330.19831268140199
2.79-2.960.22151500.17241277142798
2.97-3.190.22991470.18921340148799
3.19-3.510.24271440.19651301144599
3.52-4.010.24071360.17961287142398
4.02-5.060.24111460.17861311145799
5.06-29.360.2751350.27011272140796
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)
10.242-0.0213-0.27180.27350.14420.7327-0.03890.04870.1498-0.0219-0.0834-0.1027-0.12520.2908-0.36170.10810.0132-0.00210.07270.01720.087827.374-11.096-6.3
20.221-0.0949-0.17350.00330.00660.25290.15190.08030.1173-0.2603-0.14320.0339-0.0801-0.1741-0.03280.52830.0651-0.01510.79470.0430.210416.394-14.002-44.8
30.9293-0.0695-0.1710.25490.14710.8756-0.1535-0.1390.31290.0708-0.13630.0281-0.5116-0.5018-0.10360.21570.0223-0.02250.0474-0.02880.196323.314-5.7917.518
40.2492-0.04220.37420.26530.15990.30650.0977-0.0617-0.03260.01180.1009-0.08460.31420.36420.08190.1174-0.00580.00340.09640.00770.134527.37911.1076.313
50.0935-0.1111-0.0590.26960.14420.3450.1275-0.3191-0.4011-0.1971-0.3213-0.0385-0.074-0.3975-0.04180.3031-0.37780.4930.82020.421-0.866716.19514.00844.57
61.0528-0.03030.22060.61260.01180.6781-0.27910.1218-0.3415-0.1438-0.23460.16250.6584-0.3237-0.11670.2106-0.01120.01650.0684-0.00510.150223.3035.805-7.551
7-0.24090.28920.3145-0.39630.34430.3013-0.13260.1023-0.11020.07290.036-0.2442-0.81660.4706-0.03320.85470.04290.01120.8468-0.03640.57663.871.212-40.671
80.0280.00640.29720.17460.00290.7422-0.46260.30860.088-0.28340.2485-0.08810.13820.2879-0.00330.7287-0.08590.11651.2661-0.06830.91519.3064.956-18.416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:76 )A3 - 76
2X-RAY DIFFRACTION2( CHAIN A AND RESID 77:94 )A77 - 94
3X-RAY DIFFRACTION3( CHAIN A AND RESID 95:126 )A95 - 126
4X-RAY DIFFRACTION4( CHAIN B AND RESID 3:76 )B3 - 76
5X-RAY DIFFRACTION5( CHAIN B AND RESID 77:94 )B77 - 94
6X-RAY DIFFRACTION6( CHAIN B AND RESID 95:126 )B95 - 126
7X-RAY DIFFRACTION7( CHAIN C AND RESID 2:103 )C2 - 103
8X-RAY DIFFRACTION8( CHAIN C AND RESID 104:126 )C104 - 126

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