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- PDB-8bg5: Crystal structure of the SARS-CoV-2 S RBD in complex with pT1631 scFV -

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Basic information

Entry
Database: PDB / ID: 8bg5
TitleCrystal structure of the SARS-CoV-2 S RBD in complex with pT1631 scFV
Components
  • Spike protein S1
  • pT1631 single-chain Fv
KeywordsPROTEIN BINDING / PROTEIN BINDING/IMMUNE SYSTEM
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pT1631 single-chain Fv
B: Spike protein S1
C: pT1631 single-chain Fv
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,1116
Polymers109,6694
Non-polymers4422
Water4,504250
1
A: pT1631 single-chain Fv
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0563
Polymers54,8342
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: pT1631 single-chain Fv
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0563
Polymers54,8342
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.075, 90.813, 154.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Antibody pT1631 single-chain Fv


Mass: 29485.396 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: 25349.047 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: isolated from a natural source / 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.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.4 Å3/Da / Density % sol: 63.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: pT1631-RBD at 15.8 mg/ml using 16 % PEG 4000, 100 mM Tris pH 8.5, 200 mM Li2SO4 as reservoir and micro seeds in 18% PEG 3350, 100 mM citrate pH 4, 200 mM Na3Cit stabilization solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→49.25 Å / Num. obs: 79963 / % possible obs: 99.75 % / Redundancy: 13.7 % / Biso Wilson estimate: 40.89 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.03156 / Rrim(I) all: 0.1174 / Net I/σ(I): 16.31
Reflection shellResolution: 2.05→2.123 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.667 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 7760 / CC1/2: 0.674 / CC star: 0.897 / Rpim(I) all: 0.4625 / Rrim(I) all: 1.731 / % possible all: 97.76

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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, 7CHO

7kgj

7cho


Resolution: 2.05→49.25 Å / SU ML: 0.251 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2166 2003 2.51 %
Rwork0.1963 77897 -
obs0.1968 79900 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.03 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 28 250 6794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076718
X-RAY DIFFRACTIONf_angle_d0.84679138
X-RAY DIFFRACTIONf_chiral_restr0.056986
X-RAY DIFFRACTIONf_plane_restr0.00711178
X-RAY DIFFRACTIONf_dihedral_angle_d6.0849938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.38071400.33435336X-RAY DIFFRACTION96.92
2.1-2.160.28821410.28085506X-RAY DIFFRACTION99.91
2.16-2.220.32041410.25365472X-RAY DIFFRACTION99.98
2.22-2.290.25051420.22915539X-RAY DIFFRACTION100
2.29-2.370.25581420.22665528X-RAY DIFFRACTION100
2.37-2.470.24821400.22955516X-RAY DIFFRACTION100
2.47-2.580.25841410.21585546X-RAY DIFFRACTION99.98
2.58-2.720.25851430.21475557X-RAY DIFFRACTION100
2.72-2.890.2681400.20535552X-RAY DIFFRACTION100
2.89-3.110.23961430.20795571X-RAY DIFFRACTION100
3.11-3.420.20851440.20175579X-RAY DIFFRACTION100
3.43-3.920.17891460.18145641X-RAY DIFFRACTION100
3.92-4.940.16751450.15235669X-RAY DIFFRACTION100
4.94-49.250.19851550.18685885X-RAY DIFFRACTION99.83
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)
11.07602690308-0.66598610856-0.3058746216533.02215545817-0.01353259901982.009583021190.05240537133040.1006385027810.0681321464547-0.2278347673120.01264880744820.215961031638-0.1259040136210.016512858089-0.06149316024990.2492955969590.00620392021099-0.01711182382790.2509598642240.03121378976590.2869155097574.459794132671.06400664258-11.803336184
21.26169525772-0.161164445880.2675090047881.43495479122-0.2522616414832.162518021950.0219869854373-0.02303755613940.01229421676020.1935879071220.06393279782190.162106665604-0.0496500289908-0.000557210415897-0.09420284826190.268541280072-0.00989438883820.06098042546620.2711761744970.006851437229340.28796490964910.1776009285-12.293039632316.9011501882
31.091034949140.559339786127-0.2038438875183.28473097458-0.4231765282691.853582385970.030128652149-0.1024205595680.05442773788560.1649317878860.00482916131031-0.0313209055361-0.0902254074208-0.057367411815-0.03678274957540.209929891129-0.01001179748840.002754233513910.239027584014-0.01599648271780.22418875326342.9530027516-1.656181935426.81961073934
41.820252683640.05607119019491.093569113750.967353995872-0.204047597221.946019236530.0501393830630.101386987405-0.0403076012889-0.1866220659150.00328942752132-0.06875346380310.08545507428110.0288164504048-0.05785224005920.2900718570320.02054312386230.04443416798410.280208202309-0.004698179484650.25023648704636.9025810396-8.36799765618-23.9807042374
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 2 through 245)AA2 - 2451 - 225
22(chain 'B' and resid 334 through 1000)BB - C334 - 10001
33(chain 'C' and resid 2 through 245)CD2 - 2451 - 225
44(chain 'D' and resid 334 through 1000)DE - F334 - 10001

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