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- PDB-8bg2: Crystal structure of the SARS-CoV-2 S RBD in complex with pT1580 scFV -

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Basic information

Entry
Database: PDB / ID: 8bg2
TitleCrystal structure of the SARS-CoV-2 S RBD in complex with pT1580 scFV
Components
  • Spike protein S1
  • pT1375 single-chain Fv
KeywordsPROTEIN BINDING / PROTEIN BINDING/IMMUNE SYSTEM
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / 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 / membrane / identical protein binding / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHansen, G. / Ssebyatika, G.L. / Krey, T.
Funding support Germany, 6items
OrganizationGrant numberCountry
Other government14-76103-184 CORONA-12/20 Germany
Other government14-76103-184 CORONA-15/20 Germany
German Federal Ministry for Education and ResearchCOVIM (FKZ: 01KX2021) Germany
German Federal Ministry for Education and ResearchRAPID (FKZ: 01KI1723G) Germany
German Research Foundation (DFG)EXC 2155 Germany
German Research Foundation (DFG)2485 VIPER (398066876/GRK 2485/1) Germany
CitationJournal: To be published
Title: Activity of broadly neutralizing antibodies against sarbecoviruses: a trade-off between SARS-CoV-2 variants and distant coronaviruses?
Authors: Stein, C.S. / Hansen, G. / Ssebyatika, G.L. / Stroeh, L. / Benecke, T. / Menz, S. / Waldmann, J.-Y. / Vollmer, B. / Tipp, S. / Ochulor, O. / Herold, E. / Schwarzloh, B. / Mutschall, D. / ...Authors: Stein, C.S. / Hansen, G. / Ssebyatika, G.L. / Stroeh, L. / Benecke, T. / Menz, S. / Waldmann, J.-Y. / Vollmer, B. / Tipp, S. / Ochulor, O. / Herold, E. / Schwarzloh, B. / Mutschall, D. / Zischke, J.-Y. / Cordes, A. / Puppe, W. / Schneider, T. / Hinrichs, I. / Blasczyk, R. / Kleine-Weber, H. / Hoffmann, M. / Hoeper, M. / Kaiser, F.K. / Gonzalez-Hernandez, M. / Armando, F.K. / Ciurkiewicz, M. / Beythien, G. / Poehlmann, S. / Baumgaertner, W. / Gruenewald, K. / Osterhaus, A. / Schulz, T. / Krey, T.
History
DepositionOct 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pT1375 single-chain Fv
B: Spike protein S1
C: pT1375 single-chain Fv
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9286
Polymers97,4864
Non-polymers4422
Water7,945441
1
A: pT1375 single-chain Fv
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9643
Polymers48,7432
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-0 kcal/mol
Surface area18410 Å2
MethodPISA
2
C: pT1375 single-chain Fv
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9643
Polymers48,7432
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint0 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.046, 85.900, 88.198
Angle α, β, γ (deg.)90.000, 117.040, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody pT1375 single-chain Fv / pT1375 scFV


Mass: 26381.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly)
#2: Protein Spike protein S1


Mass: 22361.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P0DTC2
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: pT1580-RBD at 9,8 mg/ml using 1.4 M Na-Tartrate, 100 mM Tris pH 8.5 as reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45.76 Å / Num. obs: 234717 / % possible obs: 94.11 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.69 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.09489 / Rpim(I) all: 0.05927 / Rrim(I) all: 0.1123 / Net I/σ(I): 9.19
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 5914 / CC1/2: 0.444 / CC star: 0.784 / Rpim(I) all: 0.7422 / Rrim(I) all: 1.424 / % possible all: 88.15

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KGJ, 7K8M

7kgj

7k8m


Resolution: 2.1→45.76 Å / SU ML: 0.2757 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 25.3512
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 1237 1.94 %
Rwork0.189 62413 -
obs0.1898 63650 94.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.44 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6506 0 28 441 6975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726698
X-RAY DIFFRACTIONf_angle_d0.88489098
X-RAY DIFFRACTIONf_chiral_restr0.0536978
X-RAY DIFFRACTIONf_plane_restr0.00731178
X-RAY DIFFRACTIONf_dihedral_angle_d6.4097946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.34951420.31646457X-RAY DIFFRACTION88.41
2.18-2.280.33071180.28986643X-RAY DIFFRACTION90.24
2.28-2.40.29631360.24886682X-RAY DIFFRACTION91.27
2.4-2.550.27351340.23216721X-RAY DIFFRACTION91.67
2.55-2.750.25541420.21277033X-RAY DIFFRACTION95.91
2.75-3.030.26311460.2037163X-RAY DIFFRACTION97.43
3.03-3.470.2351360.17847234X-RAY DIFFRACTION97.93
3.47-4.370.17051380.157182X-RAY DIFFRACTION96.86
4.37-45.760.19091450.1587298X-RAY DIFFRACTION97.23
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)
13.91862052793-0.721704175874-0.4202680187513.073315436060.374571648441.50880265660.06676469202870.246565704169-0.251981453823-0.178765595542-0.04374174455870.2230150295240.0376529592004-0.109436793996-0.03308284028790.256398884456-0.000672347166045-0.02072911997950.1838473875270.004609903859990.160528248189-48.386286778934.14945982221.26801630978
22.85856040674-0.3216405524450.4745601165371.970693149080.124300766591.513941186890.00250277254891-0.1857874021620.3136589848220.0489950692169-0.00602427262694-0.258611091077-0.1614355873040.07407627085530.001783001694870.239966173492-0.00955521197420.02989394063440.168005466378-6.77835079681E-60.261306448514-34.293946551458.395892744718.3051139727
31.818287380290.139804436840.5701779940652.67479964557-1.158618643723.69803514333-0.0340139403317-0.04170403339220.1190364414040.153156673182-0.043562406678-0.227206757646-0.1513057872440.2662825725130.06490956343230.1764445637070.01145088487580.0205751565830.186467876501-0.03377282361170.2424727715224.891758428377.826702943644.0440867446
42.354409902750.1901006534180.808481239532.25640593447-0.4258729983911.79141891344-0.0401916200091-0.145350845541-0.219821293562-0.1667406130410.0542161257720.1724096968460.2667409791-0.231478879128-0.01138412153830.256496265386-0.009255796802060.01226774695450.203329195094-0.00198103706180.2120193218352.9248206316453.764106064140.2792830168
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1 through 245)AA1 - 2451 - 227
22(chain 'B' and resid 335 through 527)BB335 - 5271 - 193
33(chain 'C' and resid 1 through 245)CD1 - 2451 - 227
44(chain 'D' and resid 335 through 527)DE335 - 5271 - 193

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