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- PDB-7kn3: Crystal structure of SARS-CoV-2 spike protein receptor-binding do... -

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Basic information

Entry
Database: PDB / ID: 7kn3
TitleCrystal structure of SARS-CoV-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody S-B8 Fab
Components
  • S-B8 Fab heavy chain
  • S-B8 Fab light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Antibody / Spike / Coronavirus / COVID-19 / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex / phage display / pre-pandemic
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsLiu, H. / Zhu, X. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: Adv Sci / Year: 2022
Title: Neutralizing Antibodies to SARS-CoV-2 Selected from a Human Antibody Library Constructed Decades Ago.
Authors: Qiang, M. / Ma, P. / Li, Y. / Liu, H. / Harding, A. / Min, C. / Wang, F. / Liu, L. / Yuan, M. / Ji, Q. / Tao, P. / Shi, X. / Li, Z. / Li, T. / Wang, X. / Zhang, Y. / Wu, N.C. / Lee, C.D. / ...Authors: Qiang, M. / Ma, P. / Li, Y. / Liu, H. / Harding, A. / Min, C. / Wang, F. / Liu, L. / Yuan, M. / Ji, Q. / Tao, P. / Shi, X. / Li, Z. / Li, T. / Wang, X. / Zhang, Y. / Wu, N.C. / Lee, C.D. / Zhu, X. / Gilbert-Jaramillo, J. / Zhang, C. / Saxena, A. / Huang, X. / Wang, H. / James, W. / Dwek, R.A. / Wilson, I.A. / Yang, G. / Lerner, R.A.
History
DepositionNov 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 12, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 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
B: Spike protein S1
H: S-B8 Fab heavy chain
L: S-B8 Fab light chain
M: S-B8 Fab heavy chain
N: S-B8 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,61820
Polymers147,1866
Non-polymers1,43114
Water7,945441
1
A: Spike protein S1
H: S-B8 Fab heavy chain
L: S-B8 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,55512
Polymers73,5933
Non-polymers9629
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-36 kcal/mol
Surface area27900 Å2
MethodPISA
2
B: Spike protein S1
M: S-B8 Fab heavy chain
N: S-B8 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0638
Polymers73,5933
Non-polymers4695
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-21 kcal/mol
Surface area28110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.564, 191.564, 117.371
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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Antibody , 2 types, 4 molecules HMLN

#2: Antibody S-B8 Fab heavy chain


Mass: 23225.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody S-B8 Fab light chain


Mass: 24271.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Spike protein S1


Mass: 26095.348 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 / Production host: Trichoplusia ni (cabbage looper) / 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.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 4 types, 453 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 20% PEG 3350, 0.2 M sodium sulfate, pH 6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 74079 / % possible obs: 97.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.04 / Rrim(I) all: 0.106 / Χ2: 0.852 / Net I/σ(I): 6 / Num. measured all: 475304
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.32.60.44636220.7750.2850.5340.38571.4
2.3-2.363.30.46345560.7820.2690.540.39190.6
2.36-2.424.40.46950280.8480.2390.530.40198.5
2.42-2.55.90.45351070.8970.2010.4970.41199.9
2.5-2.586.70.39649900.9390.1640.4290.416100
2.58-2.6770.32151100.9610.130.3470.423100
2.67-2.7770.26150520.9680.1060.2830.451100
2.77-2.96.70.20450730.9780.0850.2220.502100
2.9-3.056.60.1550610.9860.0630.1630.596100
3.05-3.247.20.11951360.990.0470.1290.756100
3.24-3.57.90.09550310.9940.0360.1010.989100
3.5-3.857.80.07950540.9950.030.0851.201100
3.85-4.470.06851300.9950.0280.0741.46399.9
4.4-5.557.40.06250210.9960.0240.0671.606100
5.55-507.40.05951080.9980.0230.0641.612100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JMW

7jmw


Resolution: 2.251→47.908 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 3821 5.16 %
Rwork0.1863 70237 -
obs0.1881 74058 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.16 Å2 / Biso mean: 42.6689 Å2 / Biso min: 19.22 Å2
Refinement stepCycle: final / Resolution: 2.251→47.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9667 0 87 441 10195
Biso mean--61 42.91 -
Num. residues----1266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.251-2.27920.35031180.2914173567
2.2792-2.30920.29771090.2694210477
2.3092-2.34090.2942970.2509242890
2.3409-2.37430.31651300.2432250996
2.3743-2.40970.27821490.2316263699
2.4097-2.44740.27941280.22992710100
2.4474-2.48750.26881500.22522671100
2.4875-2.53040.27391060.22512706100
2.5304-2.57640.28031700.23062641100
2.5764-2.6260.27111240.23432733100
2.626-2.67960.29321720.22752644100
2.6796-2.73780.25782000.2322643100
2.7378-2.80150.23141120.22042682100
2.8015-2.87160.28081140.22142695100
2.8716-2.94920.271560.21882688100
2.9492-3.0360.25691220.21412688100
3.036-3.13390.24661000.21412696100
3.1339-3.24590.29821690.21542692100
3.2459-3.37580.1974942650100
3.3758-3.52940.23731320.18682733100
3.5294-3.71550.21742260.1792568100
3.7155-3.94810.19651910.1652633100
3.9481-4.25280.19241980.14612629100
4.2528-4.68040.1581960.12872758100
4.6804-5.35690.15241880.13352617100
5.3569-6.74620.18781800.1622632100
6.7462-47.90.1657900.1585271699
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)
12.24420.320.33363.19221.49752.08820.1093-0.0131-0.1285-0.0582-0.20.3157-0.0082-0.23030.08460.2320.0471-0.04090.248-0.03290.304-41.455-28.77135.469
22.79331.8149-0.72762.453-0.99452.1180.0759-0.1602-0.1438-0.01430.0037-0.202-0.04190.2174-0.06870.3090.06640.08010.3116-0.03740.4156-54.393-25.96369.138
30.7478-0.3984-0.12622.60620.08050.2991-0.04320.06690.03360.08380.074-0.21380.0594-0.03-0.01850.2075-0.04130.01560.2658-0.04410.2082-31.4917.11645.332
40.6350.25230.16252.3426-0.4790.1716-0.06340.22390.0089-0.4976-0.0137-0.14640.1382-0.04530.06590.3382-0.03980.09770.3163-0.0290.2-27.58221.92428.691
50.7345-0.45180.18512.2151-0.56290.45090.0052-0.00210.03140.18770.07040.1651-0.1126-0.023-0.07390.2756-0.02110.03210.3428-00.2493-65.617-71.37980.934
60.74770.04030.02722.84770.07630.16760.06080.1848-0.0181-0.3667-0.03520.0699-0.0659-0.0682-0.01790.29810.0105-0.00870.3126-0.00290.1692-66.778-77.5763.886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 334:527 )A334 - 527
2X-RAY DIFFRACTION2( CHAIN B AND RESID 334:528 )B334 - 528
3X-RAY DIFFRACTION3( CHAIN H AND RESID 1:216 )H1 - 216
4X-RAY DIFFRACTION4( CHAIN L AND RESID 1:215 )L1 - 215
5X-RAY DIFFRACTION5( CHAIN M AND RESID 1:215 )M1 - 215
6X-RAY DIFFRACTION6( CHAIN N AND RESID 1:215 )N1 - 215

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