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- PDB-8fi9: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 8fi9
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5001
Components
  • (WRAIR-5001 Fab ...) x 2
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / viral protein / SARS-CoV-2 / coronavirus / immune system / antibody / nonhuman primate / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / entry receptor-mediated virion attachment to host cell / membrane fusion / 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 speciesSevere acute respiratory syndrome coronavirus 2
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsSankhala, R.S. / Jensen, J.L. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-18-2-0040 United States
CitationJournal: Nat Commun / Year: 2024
Title: Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques.
Authors: Sankhala, R.S. / Lal, K.G. / Jensen, J.L. / Dussupt, V. / Mendez-Rivera, L. / Bai, H. / Wieczorek, L. / Mayer, S.V. / Zemil, M. / Wagner, D.A. / Townsley, S.M. / Hajduczki, A. / Chang, W.C. ...Authors: Sankhala, R.S. / Lal, K.G. / Jensen, J.L. / Dussupt, V. / Mendez-Rivera, L. / Bai, H. / Wieczorek, L. / Mayer, S.V. / Zemil, M. / Wagner, D.A. / Townsley, S.M. / Hajduczki, A. / Chang, W.C. / Chen, W.H. / Donofrio, G.C. / Jian, N. / King, H.A.D. / Lorang, C.G. / Martinez, E.J. / Rees, P.A. / Peterson, C.E. / Schmidt, F. / Hart, T.J. / Duso, D.K. / Kummer, L.W. / Casey, S.P. / Williams, J.K. / Kannan, S. / Slike, B.M. / Smith, L. / Swafford, I. / Thomas, P.V. / Tran, U. / Currier, J.R. / Bolton, D.L. / Davidson, E. / Doranz, B.J. / Hatziioannou, T. / Bieniasz, P.D. / Paquin-Proulx, D. / Reiley, W.W. / Rolland, M. / Sullivan, N.J. / Vasan, S. / Collins, N.D. / Modjarrad, K. / Gromowski, G.D. / Polonis, V.R. / Michael, N.L. / Krebs, S.J. / Joyce, M.G.
History
DepositionDec 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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: Spike protein S1
C: Spike protein S1
F: WRAIR-5001 Fab Light chain
G: WRAIR-5001 Fab Heavy chain
H: WRAIR-5001 Fab Heavy chain
I: WRAIR-5001 Fab Light chain
J: WRAIR-5001 Fab Heavy chain
K: Spike protein S1
L: WRAIR-5001 Fab Light chain
N: WRAIR-5001 Fab Light chain
O: Spike protein S1
Q: WRAIR-5001 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,46226
Polymers280,65612
Non-polymers1,80614
Water724
1
A: Spike protein S1
H: WRAIR-5001 Fab Heavy chain
L: WRAIR-5001 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5696
Polymers70,1643
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Spike protein S1
F: WRAIR-5001 Fab Light chain
G: WRAIR-5001 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3854
Polymers70,1643
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: WRAIR-5001 Fab Light chain
J: WRAIR-5001 Fab Heavy chain
O: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5696
Polymers70,1643
Non-polymers4053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
K: Spike protein S1
N: WRAIR-5001 Fab Light chain
Q: WRAIR-5001 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,93810
Polymers70,1643
Non-polymers7747
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.508, 115.565, 142.167
Angle α, β, γ (deg.)90.00, 111.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 8 molecules FILNGHJQ

#2: Antibody
WRAIR-5001 Fab Light chain


Mass: 22972.252 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Antibody
WRAIR-5001 Fab Heavy chain


Mass: 24118.041 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 8 molecules ACKO

#1: Protein
Spike protein S1


Mass: 23073.766 Da / Num. of mol.: 4 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#4: 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.: 4 / 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

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Non-polymers , 2 types, 14 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M Phosphate-citrate pH 4.5, 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.19→87.31 Å / Num. obs: 31815 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.981 / Net I/σ(I): 1.1
Reflection shellResolution: 4.19→4.42 Å / Num. unique obs: 4553 / CC1/2: 0.348

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→19.99 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2958 1550 5 %
Rwork0.2521 --
obs0.2543 30971 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17835 0 116 4 17955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318398
X-RAY DIFFRACTIONf_angle_d0.6125061
X-RAY DIFFRACTIONf_dihedral_angle_d6.8242583
X-RAY DIFFRACTIONf_chiral_restr0.0462754
X-RAY DIFFRACTIONf_plane_restr0.0043237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.330.38371460.36362628X-RAY DIFFRACTION100
4.33-4.490.38931330.3382656X-RAY DIFFRACTION100
4.49-4.660.32081390.29862692X-RAY DIFFRACTION100
4.66-4.870.3681450.29272639X-RAY DIFFRACTION100
4.87-5.130.31111380.292667X-RAY DIFFRACTION100
5.13-5.440.33251410.27542687X-RAY DIFFRACTION100
5.44-5.850.311390.26732645X-RAY DIFFRACTION100
5.85-6.420.32921410.27222692X-RAY DIFFRACTION100
6.42-7.310.27951400.26132685X-RAY DIFFRACTION100
7.31-9.070.29881410.22722689X-RAY DIFFRACTION100
9.07-19.990.22541470.19182741X-RAY DIFFRACTION100
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)
14.7805-1.4244.74243.108-2.97636.8008-0.6044-0.07130.22230.04920.09970.4017-0.0051-1.09740.60722.1576-0.11570.08582.1245-0.1871.9528.708615.54266.4311
27.0184-3.78813.36335.3883-1.59844.2655-0.44810.54740.03210.188-0.11510.2863-0.37460.1280.4951.9994-0.16630.09441.93970.0591.845722.397424.569259.5192
38.0706-2.6512-0.94656.03860.75739.1550.1394-0.2216-0.9124-0.5117-0.5124-0.02770.00310.46220.312.11790.0052-0.02282.0450.06371.953169.4436-13.691653.7341
43.4043-2.27974.01527.3073-7.24957.5579-0.77290.14980.87940.1874-0.6525-0.7065-0.89460.99381.4523.25220.2752-0.25563.21430.07472.237466.968217.80824.3216
57.4638-1.6813-0.71026.97921.75737.3484-0.1375-0.4426-0.0641-0.5418-0.08370.02610.25280.33850.24271.59480.0501-0.0771.05570.12971.63347.90150.481583.4198
63.4168-1.1852.08724.1548-3.73634.8008-0.4346-0.4044-0.01680.30050.62160.4499-0.5374-0.44410.06782.96670.30560.10132.9351-0.08271.841349.812613.674624.0643
75.15581.7897-2.51844.7247-0.26465.67830.3635-0.03150.40450.67-1.15641.09380.7382-0.70060.68181.8729-0.264-0.02822.2403-0.35182.3552138.18511.969694.9415
85.84742.49911.54514.36190.20934.8237-0.68410.0065-1.30550.7752-0.55280.60541.0447-1.74341.07892.6737-0.52480.7382.7826-0.8063.3182119.2911-6.8647101.6147
97.1617-5.4544-1.61864.6764-0.28965.5932-0.0315-0.18180.59020.5044-0.12820.0701-0.8849-0.18760.13322.8429-0.2659-0.19912.6196-0.31272.339396.610927.795126.2279
103.73713.99221.364.44843.07222.94640.3792-1.33691.00820.4666-0.5060.9815-0.00080.12610.01772.39810.0574-0.07653.0826-0.11732.248770.1048-5.6683116.1538
117.7454-2.43270.28063.64091.24775.2268-0.6729-1.1409-0.87910.17270.20530.38510.29270.48590.45162.3567-0.19950.14382.17960.20461.8975132.580210.8605121.2257
123.10783.14652.73396.29584.1563.4511-0.4971-0.42480.5245-0.25870.46-0.0471-0.2850.06180.02212.39540.0574-0.28182.416-0.0822.054377.4461-3.452599.9882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'L' and resid 1 through 212)
2X-RAY DIFFRACTION2(chain 'H' and resid 1 through 215)
3X-RAY DIFFRACTION3(chain 'C' and resid 333 through 530)
4X-RAY DIFFRACTION4(chain 'F' and resid 1 through 208)
5X-RAY DIFFRACTION5(chain 'A' and resid 333 through 530)
6X-RAY DIFFRACTION6(chain 'G' and resid 2 through 215)
7X-RAY DIFFRACTION7(chain 'I' and resid 2 through 108)
8X-RAY DIFFRACTION8(chain 'J' and resid 3 through 111)
9X-RAY DIFFRACTION9(chain 'K' and resid 334 through 527)
10X-RAY DIFFRACTION10(chain 'N' and resid 1 through 210)
11X-RAY DIFFRACTION11(chain 'O' and resid 332 through 527)
12X-RAY DIFFRACTION12(chain 'Q' and resid 2 through 216)

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