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- PDB-8bg4: Crystal structure of the SARS-CoV-2 S RBD in complex with pT1611 scFV -

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Basic information

Entry
Database: PDB / ID: 8bg4
TitleCrystal structure of the SARS-CoV-2 S RBD in complex with pT1611 scFV
Components
  • Spike protein S1
  • pT1611 single-chain Fv
KeywordsPROTEIN BINDING / PROTEIN BINDING/IMMUNE SYSTEM
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / 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 ...symbiont-mediated disruption of host tissue / 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 / symbiont entry into host cell / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 (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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, 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: 1.6 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 1.1Oct 16, 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: pT1611 single-chain Fv
B: Spike protein S1
C: pT1611 single-chain Fv
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5526
Polymers97,1104
Non-polymers4422
Water13,619756
1
A: pT1611 single-chain Fv
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7763
Polymers48,5552
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint4 kcal/mol
Surface area18150 Å2
MethodPISA
2
C: pT1611 single-chain Fv
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7763
Polymers48,5552
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint5 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.294, 90.946, 154.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody pT1611 single-chain Fv / pT1611 scFV


Mass: 26192.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: scFv / 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.: 756 / 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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: pT1611-RBD at 18.7 mg/ml using 1.6 M ammonium-sulfate, 2 % PEG 1000, 100 mM HEPES pH 8 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: 1.6→49 Å / Num. obs: 164051 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 22.35 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.09057 / Rpim(I) all: 0.02549 / Rrim(I) all: 0.09415 / Net I/σ(I): 21.14
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.872 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 16225 / CC1/2: 0.699 / CC star: 0.907 / Rpim(I) all: 0.5198 / Rrim(I) all: 1.944 / % possible all: 99.98

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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, 2GHW

7kgj

2ghw


Resolution: 1.6→49 Å / SU ML: 0.2262 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8126
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2077 2460 0.78 %
Rwork0.1945 313489 -
obs0.1947 163954 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.55 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6455 0 28 756 7239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626641
X-RAY DIFFRACTIONf_angle_d0.86439024
X-RAY DIFFRACTIONf_chiral_restr0.0576979
X-RAY DIFFRACTIONf_plane_restr0.00811168
X-RAY DIFFRACTIONf_dihedral_angle_d6.1205935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.37121410.359417373X-RAY DIFFRACTION99.36
1.63-1.660.361320.342717426X-RAY DIFFRACTION99.61
1.66-1.70.35791500.344917387X-RAY DIFFRACTION99.66
1.7-1.740.34541280.336817490X-RAY DIFFRACTION99.6
1.74-1.780.32941340.291717437X-RAY DIFFRACTION99.73
1.78-1.830.25631420.25817415X-RAY DIFFRACTION99.74
1.83-1.890.2321340.241117344X-RAY DIFFRACTION98.95
1.89-1.950.30651340.229117382X-RAY DIFFRACTION99.49
1.95-2.020.21651440.211817481X-RAY DIFFRACTION99.9
2.02-2.10.22711430.212417367X-RAY DIFFRACTION99.51
2.1-2.190.24041300.191217495X-RAY DIFFRACTION99.96
2.19-2.310.22321200.188117439X-RAY DIFFRACTION99.54
2.31-2.450.20691540.193417498X-RAY DIFFRACTION99.8
2.45-2.640.20431400.186917273X-RAY DIFFRACTION98.98
2.64-2.910.19171250.191617397X-RAY DIFFRACTION99.51
2.91-3.330.16751410.173517502X-RAY DIFFRACTION99.92
3.33-4.190.15331300.15717392X-RAY DIFFRACTION99.37
4.19-490.17811380.158117391X-RAY DIFFRACTION99.4
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)
11.037226010560.4996672455960.1342237889722.625253291570.1808438214411.425825613080.105602225866-0.173339248533-0.01019524980340.366782759907-0.0984334238638-0.1226584197840.0790255255923-0.0361177439235-0.002346114367910.172125789281-0.0270855700298-0.02235346870570.171205252354-0.006069859060270.17204954891784.699068001446.252316051589.4543679185
21.139236120770.1734124233380.3479432936041.537091466290.2337662674772.072789002960.003409230308560.102706229694-0.013631692064-0.127500158560.0435127468783-0.1081540648390.0386937603250.0116782795253-0.04914289088080.112052772930.008281106638030.02939395901510.1324109754320.002704552803350.13546459644778.542911317633.193338412460.5221291323
31.15100974255-0.2963389827450.2141214956182.67694606639-0.1310533525131.506109922580.06687570791470.1153563002720.00684615576436-0.226257706936-0.01700292779130.03566240396430.06960233693440.0805117829912-0.0473759181780.1463894698730.0128327829115-0.006928124049490.1662419967050.006503874887610.15841239638646.038819732943.678507543870.4064356234
41.614485908560.04669429653341.281531022980.8384023175220.03649718305522.438782379130.0485145631176-0.112355899077-0.04191285508090.1194407410440.009383030801790.007193357571270.1300412407980.0403366232874-0.05920070355520.147872145949-0.008947570252350.02741680795220.144200793964-0.01044596581360.1310832808852.076702382937.2895556283101.188899144
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 244)AA2 - 2441 - 222
22(chain 'B' and resid 334 through 1000)BB - C334 - 10001
33(chain 'C' and resid 2 through 243)CD2 - 2431 - 222
44(chain 'D' and resid 334 through 1000)DE - F334 - 10001

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