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- PDB-8hn7: Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD -

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Basic information

Entry
Database: PDB / ID: 8hn7
TitleCrystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD
Components
  • Heavy chain of monoclonal antibody 3C11
  • Light chain of monoclonal antibody 3C11
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / monoclonal antibody / RBD / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsQi, J. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Front Immunol / Year: 2023
Title: Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents.
Authors: Wang, Z. / Li, D. / Chen, Y. / Sun, Y. / Jin, C. / Hu, C. / Feng, Y. / Su, J. / Ren, L. / Hao, Y. / Wang, S. / Zhu, M. / Liu, Y. / Qi, J. / Zhu, B. / Shao, Y.
History
DepositionDec 7, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _citation.journal_volume / _citation.year / _entity.pdbx_description
Revision 1.2Jun 7, 2023Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light chain of monoclonal antibody 3C11
B: Heavy chain of monoclonal antibody 3C11
E: Spike protein S1
C: Light chain of monoclonal antibody 3C11
D: Heavy chain of monoclonal antibody 3C11
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6208
Polymers138,1786
Non-polymers4422
Water00
1
A: Light chain of monoclonal antibody 3C11
B: Heavy chain of monoclonal antibody 3C11
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3104
Polymers69,0893
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Light chain of monoclonal antibody 3C11
D: Heavy chain of monoclonal antibody 3C11
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3104
Polymers69,0893
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.387, 156.780, 94.425
Angle α, β, γ (deg.)90.000, 104.740, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody Light chain of monoclonal antibody 3C11


Mass: 23513.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others)
#2: Antibody Heavy chain of monoclonal antibody 3C11


Mass: 23702.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others)
#3: Protein Spike protein S1


Mass: 21873.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Insect cell expression vector pTIE1 (others)
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
Has ligand of interestY

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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: 3.49 Å3/Da / Density % sol: 64.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG4000,magnesium chloride, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 36958 / % possible obs: 98 % / Redundancy: 6.9 % / Biso Wilson estimate: 57.04 Å2 / CC1/2: 0.995 / Net I/σ(I): 13.2
Reflection shellResolution: 3→3.11 Å / Num. unique obs: 3756 / CC1/2: 0.912

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→21.09 Å / SU ML: 0.4139 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.8594
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2628 1759 5.02 %
Rwork0.2324 33259 -
obs0.2339 35018 92.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.99 Å2
Refinement stepCycle: LAST / Resolution: 3→21.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9726 0 28 0 9754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003410024
X-RAY DIFFRACTIONf_angle_d0.76313649
X-RAY DIFFRACTIONf_chiral_restr0.05021496
X-RAY DIFFRACTIONf_plane_restr0.00491765
X-RAY DIFFRACTIONf_dihedral_angle_d12.7763579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.3866990.3261827X-RAY DIFFRACTION66.6
3.08-3.180.35011400.30982233X-RAY DIFFRACTION81.8
3.18-3.280.33091220.30832537X-RAY DIFFRACTION91.78
3.28-3.390.30971350.29132657X-RAY DIFFRACTION96.44
3.39-3.530.31321280.27662726X-RAY DIFFRACTION99.65
3.53-3.690.30961180.29072241X-RAY DIFFRACTION82.28
3.69-3.880.31791340.27042513X-RAY DIFFRACTION91.4
3.88-4.120.27711440.23462719X-RAY DIFFRACTION99.79
4.12-4.440.25071300.19842795X-RAY DIFFRACTION99.83
4.44-4.880.1811350.1792752X-RAY DIFFRACTION99.83
4.88-5.580.19651430.19012770X-RAY DIFFRACTION99.9
5.58-6.980.29851740.22482718X-RAY DIFFRACTION99.83
6.98-21.090.20591570.19142771X-RAY DIFFRACTION98.95
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)
10.86539851472-0.450260891783-0.864780597471.30393161967-0.1364732865683.117143999010.01585769276160.150845929105-0.118036179731-0.18007500729-0.000607012516586-0.00669982878810.2366454716970.123359228406-0.03557737202620.308424809831-0.00493910993356-0.05814329497520.310968002112-0.03213616476920.34748829996427.683189468529.1030687413-36.3983527253
20.417429415074-0.1429455655060.144273591470.851120586570.6292732968052.117234897750.003157793568970.1324080108130.124042106708-0.218449933254-0.00272620824887-0.109921934179-0.1109584852940.253619808937-0.005677536050320.284169800986-0.01383599218950.0287391962490.3466212476130.02917327190420.36171439725927.730444460347.0985821139-35.0699017493
30.9988135611820.0337208956239-0.3341926266911.463895363310.4389697052032.42686154377-0.0134278895267-0.1609816721550.1714720632230.08513514509880.086427886856-0.0962492911847-0.04979295595130.0966174015124-0.1310611918310.2663462482170.00342155530398-0.02508185118250.254723515594-0.01803287919160.3888176978128.8948074539.404914284741.22492094093
40.80682301307-0.483749545045-0.3701534837420.9634581644410.005991332786141.77225767268-0.0579622975244-0.0611808135832-0.0907283429138-0.03079332532720.02201729112950.1202891352970.140430351251-0.07788156567420.01985776105720.209438183052-0.0376132312672-0.01298837816010.2631762227820.004322036816690.32858560665429.9110479922-8.667257448961.20392233013
52.44768285835-1.0711010517-0.07632900829253.17720054425-0.5548570817492.44492273108-0.273083084663-0.3899349387660.5129044962590.675596815530.069525441693-0.09665733663-0.412941779435-0.161489800720.184209962420.396184328780.0319569407533-0.04913337472110.435273666232-0.1034808584820.5006990133722.4987158244169.3078243043-3.00271307324
62.267991296951.246500459350.3888490563733.21161254589-0.1995405699852.117291381410.1628850753060.321429136076-0.545534068982-0.256989980659-0.0716243784715-0.2935052945940.2053748285370.0528787490672-0.07435575602830.5213905157270.0283873898004-0.07251857225880.502043312321-0.0929181412480.46125574384323.9956593943-31.8948007542-39.1546154239
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA3 - 2161 - 214
22chain BBB1 - 2211 - 221
33chain CCE3 - 2161 - 214
44chain DDF1 - 2211 - 221
55chain EEC - D333 - 6191
66chain FFG - H333 - 6191

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