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- PDB-8bg1: Crystal structure of the SARS-CoV-2 S RBD in complex with pT1511 scFV -

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Basic information

Entry
Database: PDB / ID: 8bg1
TitleCrystal structure of the SARS-CoV-2 S RBD in complex with pT1511 scFV
Components
  • Spike protein S1
  • pT1511 Fab heavy chain
  • pT1511 Fab light chain
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 / 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 / symbiont-mediated suppression of host innate immune response / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 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 6, 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: pT1511 Fab heavy chain
B: pT1511 Fab light chain
C: Spike protein S1
D: pT1511 Fab heavy chain
E: pT1511 Fab light chain
F: Spike protein S1
G: pT1511 Fab heavy chain
H: pT1511 Fab light chain
I: Spike protein S1
J: pT1511 Fab heavy chain
K: pT1511 Fab light chain
L: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,13616
Polymers286,69912
Non-polymers1,4374
Water00
1
A: pT1511 Fab heavy chain
B: pT1511 Fab light chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2454
Polymers71,6753
Non-polymers5711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: pT1511 Fab heavy chain
E: pT1511 Fab light chain
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0994
Polymers71,6753
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: pT1511 Fab heavy chain
H: pT1511 Fab light chain
I: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8964
Polymers71,6753
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: pT1511 Fab heavy chain
K: pT1511 Fab light chain
L: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8964
Polymers71,6753
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)345.270, 54.370, 214.690
Angle α, β, γ (deg.)90.000, 105.880, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules CFIL

#3: Protein
Spike protein S1


Mass: 22361.924 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S, 2 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P0DTC2

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Antibody , 2 types, 8 molecules ADGJBEHK

#1: Antibody
pT1511 Fab heavy chain


Mass: 25399.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686P15220 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody
pT1511 Fab light chain


Mass: 23913.615 Da / Num. of mol.: 4
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)

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Sugars , 3 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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

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Details

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: 3.38 Å3/Da / Density % sol: 63.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: pT1511-RBD at 9.5 mg/ml using 16% PEG 3350, 200 mM sodium malonate, 100 mM Bis-tris propane pH 7.5 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: Sep 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→48.83 Å / Num. obs: 85773 / % possible obs: 96.95 % / Redundancy: 6.5 % / Biso Wilson estimate: 95.53 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1365 / Rpim(I) all: 0.05722 / Rrim(I) all: 0.1484 / Net I/σ(I): 9.38
Reflection shellResolution: 2.88→2.983 Å / Rmerge(I) obs: 1.604 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 7494 / CC1/2: 0.535 / CC star: 0.835 / Rpim(I) all: 0.6858 / Rrim(I) all: 1.75

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KGJ, 4QF1

7kgj

4qf1


Resolution: 2.88→48.83 Å / SU ML: 0.5081 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.1517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2444 8259 5.01 %
Rwork0.2021 156501 -
obs0.2043 85642 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 105.21 Å2
Refinement stepCycle: LAST / Resolution: 2.88→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19547 0 94 0 19641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004420127
X-RAY DIFFRACTIONf_angle_d0.772227396
X-RAY DIFFRACTIONf_chiral_restr0.04663033
X-RAY DIFFRACTIONf_plane_restr0.00643545
X-RAY DIFFRACTIONf_dihedral_angle_d5.16192805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.910.48911590.48993053X-RAY DIFFRACTION57.02
2.91-2.950.44832780.40045246X-RAY DIFFRACTION98.05
2.95-2.980.42242800.38525330X-RAY DIFFRACTION98.25
2.98-3.020.41642850.37155409X-RAY DIFFRACTION98.38
3.02-3.060.39212740.39475179X-RAY DIFFRACTION98.38
3.06-3.10.45622720.4145196X-RAY DIFFRACTION98.22
3.1-3.150.39552780.36425330X-RAY DIFFRACTION97.84
3.15-3.190.36812710.32835096X-RAY DIFFRACTION93.26
3.19-3.240.36082710.30015291X-RAY DIFFRACTION98.62
3.24-3.30.3692810.27535266X-RAY DIFFRACTION98.91
3.3-3.350.29852850.2625344X-RAY DIFFRACTION98.93
3.35-3.410.29352810.26855384X-RAY DIFFRACTION98.99
3.41-3.480.31842740.25565249X-RAY DIFFRACTION98.82
3.48-3.550.3362800.265270X-RAY DIFFRACTION98.86
3.55-3.630.29962810.24015435X-RAY DIFFRACTION98.67
3.63-3.710.26122780.20915238X-RAY DIFFRACTION99.07
3.71-3.810.27142790.19735317X-RAY DIFFRACTION98.99
3.81-3.910.22142850.19755401X-RAY DIFFRACTION99.15
3.91-4.020.24322730.19585262X-RAY DIFFRACTION99
4.02-4.150.2822880.18685427X-RAY DIFFRACTION99.15
4.15-4.30.1892740.17115188X-RAY DIFFRACTION98.63
4.3-4.470.18972810.16055374X-RAY DIFFRACTION98.48
4.47-4.680.21532740.15955055X-RAY DIFFRACTION95.31
4.68-4.920.17482870.14855391X-RAY DIFFRACTION98.68
4.92-5.230.19122790.15075272X-RAY DIFFRACTION99.5
5.23-5.630.25762840.16695374X-RAY DIFFRACTION99.4
5.64-6.20.21742800.18195315X-RAY DIFFRACTION99.4
6.2-7.10.23952830.18145373X-RAY DIFFRACTION99.35
7.1-8.930.2062830.17285312X-RAY DIFFRACTION98.49
8.93-48.830.18042810.175124X-RAY DIFFRACTION95.51
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)
13.430573236991.3370315012-0.4829824694510.758984406803-0.5718139388290.8692781759120.0661221274335-0.1709868533340.3857294126310.0949565651557-0.038627358150.263100433254-0.1125504831360.189250368332-0.029687039770.841718531989-0.01566490729420.06311931767080.451927556493-0.1699501788560.79601504274571.9212892871-2.0675781312280.8370268984
24.442916652972.37556589115-0.1851040180671.2155555851-0.3091046961211.223031095-0.0943494277095-0.0498113318784-0.704533133362-0.01222604238710.0170622371726-0.3427057711140.02642956648730.3903302575080.03462944998950.790028186296-0.0007875713025380.07228645866360.512904166335-0.1172342768560.9211963088286.9047672924-12.723203933383.4908033854
32.87819039014-0.5225891138331.372463423971.48782887171-0.3638162150644.54697463329-0.02692327645130.151607286535-0.169600021979-0.06649443807370.106629430356-0.06508676550020.164399703331-0.478680236152-0.04230978030990.834109950482-0.1249053934930.03040386948810.615055273479-0.02589479217830.82734872751639.7716582001-28.683071730263.8730532233
43.67696066549-1.462812320540.2674983596810.7199106350780.1127252212960.414930905820.07615641625370.3618329690930.2380579583-0.0973625929014-0.131258782034-0.170749143206-0.1701922309360.07116023101680.0471142711390.84609046568-0.112475582222-0.01183551321740.6885863269880.1160926816670.79718627747471.244824804821.998482669921.1980388584
53.7713719802-2.142236649370.5368232835381.5150166249-0.01402835187271.225392729620.07522675010280.396408609709-0.39521348029-0.0157076883296-0.1290188783210.1477602266490.0153503672566-0.2102213048370.05784273295980.739646651788-0.134194780894-0.009130767425340.670769367290.01258727835680.79642564794456.724289705610.593513493219.8945901008
62.322893440180.6447049176211.326226169672.218696221080.6446194712374.23545679793-0.0668969322463-0.00944713642103-0.01697246917230.1396579224150.05180534367140.07500963860390.08529679349380.4544283616020.03502106080360.6691082920990.003920454676510.02525412263920.867643639902-0.01335698182020.794362640049104.44803303-1.0853736417539.8531945926
72.709521407650.4331289704672.596528252070.6832534423850.7631345806472.608269616930.109235682501-0.66259173462-0.5717000584980.06191477510840.08624904486790.00140798392636-0.0190173773144-0.525598648131-0.1410956630470.7723672584310.04677421814830.05446188468541.235573105950.2522543037541.03727273919-28.675865585-32.644996780469.7403952452
83.298031553310.406509542422.175873151350.8485623260950.8033799710392.4315739448-0.4096859401710.0434042895820.1560226967170.1354547067330.1821014059-0.0398822878023-0.306441542901-0.02644360566540.2809740574231.025206956710.08538323686980.0171741743271.118594347410.1242886438280.910419477618-31.7958509509-18.676669311557.1342108531
93.54157760626-0.546854502340.9309764343932.76211415399-0.5337674219891.91656424798-0.304494028889-0.5137646265850.1549328846050.04043748844070.04155987307740.129674128714-0.318852516625-0.2407822174650.2359773723871.065731950530.210517206026-0.04120574376991.253020059350.04620538976060.8465579639293.7255235937-19.375360994796.7862090521
103.44785178817-0.07787590003373.029386982350.971400850624-0.3213891256822.641457849490.3200647327120.766434064211-0.555357544698-0.0283155150602-0.05325015082540.09318591448260.1675048148560.320906983563-0.2358743032990.775236602978-0.1055192076770.01643489527941.31421948496-0.248820400080.929681593818-0.0523308822041-35.379783182134.8498925362
113.26903116090.04013283498692.837362784620.176959422293-0.2121016479713.25450333987-0.3201970591870.150738604440.224539143999-0.0767830754710.05474835644440.080980245574-0.350393659885-0.1377362164570.2539445389710.891564681897-0.160546244161-0.03460348383981.00959139686-0.08127258448480.8013610173553.60705942896-20.327800452346.2679221124
123.99204290710.6211022955380.502269797512.292475096080.5358114517122.31582300605-0.2950588471890.5289396413920.118026386909-0.02566691607970.126535552153-0.131425618693-0.2724265475340.3300719625760.1798198181010.919769447678-0.141089074759-0.07552792807041.361996690530.01559133775140.725360658294-32.0213141947-23.94469890646.75008539836
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 220)AA1 - 2201 - 227
22(chain 'B' and resid 2 through 216)BB2 - 2161 - 215
33(chain 'C' and resid 334 through 528)CC334 - 5281 - 195
44(chain 'D' and resid 1 through 220)DD1 - 2201 - 227
55(chain 'E' and resid 2 through 216)EE2 - 2161 - 215
66(chain 'F' and resid 334 through 528)FF334 - 5281 - 195
77(chain 'G' and resid 1 through 220)GG1 - 2201 - 221
88(chain 'H' and resid 2 through 216)HH2 - 2161 - 215
99(chain 'I' and resid 334 through 528)II334 - 5281 - 195
1010(chain 'J' and resid 1 through 219)JJ1 - 2191 - 220
1111(chain 'K' and resid 2 through 216)KK2 - 2161 - 215
1212(chain 'L' and resid 335 through 528)LL335 - 5281 - 194

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