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- PDB-8hn6: Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD -

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Basic information

Entry
Database: PDB / ID: 8hn6
TitleCrystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD
Components
  • Heavy chain of monoclonal antibody 3G10
  • Light chain of monoclonal antibody 3G10
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / RBD / monoclonal antibody / 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 / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 ...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 / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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 / Structure summary / Category: citation / citation_author / entity
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: Heavy chain of monoclonal antibody 3G10
B: Light chain of monoclonal antibody 3G10
E: Spike protein S1
C: Heavy chain of monoclonal antibody 3G10
D: Light chain of monoclonal antibody 3G10
F: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)92,7406
Polymers92,7406
Non-polymers00
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-39 kcal/mol
Surface area32820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.680, 105.730, 209.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-221-

HOH

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Components

#1: Antibody Heavy chain of monoclonal antibody 3G10


Mass: 12665.165 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Light chain of monoclonal antibody 3G10


Mass: 11831.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350,0.1 M HEPES,0.2 M LProline

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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: 2.07→28.65 Å / Num. obs: 66979 / % possible obs: 99.9 % / Redundancy: 12.3 % / Biso Wilson estimate: 35.7 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.7
Reflection shellResolution: 2.07→2.12 Å / Num. unique obs: 4877 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→26.43 Å / SU ML: 0.2133 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1513
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2143 3111 4.67 %
Rwork0.192 63558 -
obs0.193 66669 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.43 Å2
Refinement stepCycle: LAST / Resolution: 2.07→26.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6499 0 0 505 7004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836668
X-RAY DIFFRACTIONf_angle_d1.09699066
X-RAY DIFFRACTIONf_chiral_restr0.0752985
X-RAY DIFFRACTIONf_plane_restr0.00641171
X-RAY DIFFRACTIONf_dihedral_angle_d13.26822364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.10.30361300.28182790X-RAY DIFFRACTION98.42
2.1-2.140.31461450.2722854X-RAY DIFFRACTION99.34
2.14-2.170.29311540.25372819X-RAY DIFFRACTION99.23
2.17-2.210.26161350.25612868X-RAY DIFFRACTION99.34
2.21-2.260.31211350.23692886X-RAY DIFFRACTION99.31
2.26-2.30.23481290.24132840X-RAY DIFFRACTION99.5
2.3-2.350.27351370.24042878X-RAY DIFFRACTION99.37
2.35-2.410.25191500.22932879X-RAY DIFFRACTION99.57
2.41-2.470.26481420.2322839X-RAY DIFFRACTION99.63
2.47-2.530.26351390.22142853X-RAY DIFFRACTION99.44
2.53-2.610.27161570.22042868X-RAY DIFFRACTION99.67
2.61-2.690.24941570.23762865X-RAY DIFFRACTION99.74
2.69-2.790.25611340.22282899X-RAY DIFFRACTION99.77
2.79-2.90.24941460.20432880X-RAY DIFFRACTION99.61
2.9-3.030.23891250.20732909X-RAY DIFFRACTION99.9
3.03-3.190.24411290.19652916X-RAY DIFFRACTION99.97
3.19-3.390.20051420.19262901X-RAY DIFFRACTION99.9
3.39-3.650.18951570.18192909X-RAY DIFFRACTION99.97
3.65-4.020.19541340.16332933X-RAY DIFFRACTION99.97
4.02-4.60.15211360.14262944X-RAY DIFFRACTION100
4.6-5.780.17231490.14832955X-RAY DIFFRACTION99.94
5.78-26.430.18051490.18333073X-RAY DIFFRACTION99.29
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)
11.31169403921-0.05330221624710.3391989997312.49653755092-0.9317293184671.66773566260.06553871444740.16304866177-0.221030544714-0.387655639953-0.07529967470580.1218278431570.388420940515-0.08956688975510.02655249633590.412970843740.00384217979157-0.02209322205420.317594885229-0.06013079072210.34383945835-39.7219759922-20.812526658-20.888390718
22.308716864010.283575425683-0.189499011981.80602434735-0.8432101149172.522561679360.0137837921201-0.0989210546664-0.04401394884880.0693624158523-0.0652712796074-0.01163042405260.05179076852-0.07362857851130.05573845747750.254084427949-0.008133162578840.007569874823720.25435747803-0.02626095378010.270518528027-31.8647155716-14.8007556866-0.899243333946
31.67336929885-0.4355762279490.22647231171.25091903325-0.7461795409662.84268582746-0.03287578875790.1568080485150.0418359159334-0.05138814110550.1326033435610.1418648482590.0634561964932-0.181692128401-0.1017637439660.279157262245-0.0104442717392-0.01173865523910.3288611102820.008610761713670.305457368116-10.2836030476-23.8961365273-42.3955892255
41.91848328656-0.276199316656-0.7671986668062.435077721190.3063373112753.332726024870.0746165801274-0.04215512417510.141273754364-0.008044821362980.0934658560459-0.0674859582655-0.2191638112760.181035982776-0.1746049022660.280631792551-0.02043441741250.006757902081380.287088378353-0.03544027769590.2903137262454.67526175943-9.27833917139-34.667104737
52.64939771502-0.321002811726-1.294642326170.812182259163-0.06545941507622.182334166260.1481464787580.0674738622510.266093630274-0.158301539984-0.097176432236-0.106636574858-0.2160082803560.134141427996-0.06197009948380.3510542995130.0443614566220.03149692764790.2823666318240.01808997608660.341005860266-21.00097693854.97506317748-27.7653452476
61.86685767024-0.224394528904-1.131842898850.954905727880.1243279453011.66792593287-0.0785703101478-0.185360807997-0.06190055294320.2187632223860.04942542935680.06607622131480.1155548119920.02858383734740.0311152829070.3273714140070.0600025698145-0.01739627662640.312739862640.005012867367010.278274781455-8.87746147692-30.6542137457-10.3599453003
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA2 - 1171 - 116
22chain BBB0 - 1071 - 108
33chain CCD2 - 1181 - 117
44chain DDE0 - 1071 - 108
55chain EEC333 - 5271 - 195
66chain FFF333 - 5271 - 195

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