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- PDB-7bwj: crystal structure of SARS-CoV-2 antibody with RBD -

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Basic information

Entry
Database: PDB / ID: 7bwj
Titlecrystal structure of SARS-CoV-2 antibody with RBD
Components
  • Spike protein S1
  • antibody heavy chainImmunoglobulin heavy chain
  • antibody light chainImmunoglobulin light chain
KeywordsVIRAL PROTEIN / spike / receptor binding domain / antibody
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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsWang, X. / Ge, J.
CitationJournal: Nature / Year: 2020
Title: Human neutralizing antibodies elicited by SARS-CoV-2 infection.
Authors: Ju, B. / Zhang, Q. / Ge, J. / Wang, R. / Sun, J. / Ge, X. / Yu, J. / Shan, S. / Zhou, B. / Song, S. / Tang, X. / Yu, J. / Lan, J. / Yuan, J. / Wang, H. / Zhao, J. / Zhang, S. / Wang, Y. / ...Authors: Ju, B. / Zhang, Q. / Ge, J. / Wang, R. / Sun, J. / Ge, X. / Yu, J. / Shan, S. / Zhou, B. / Song, S. / Tang, X. / Yu, J. / Lan, J. / Yuan, J. / Wang, H. / Zhao, J. / Zhang, S. / Wang, Y. / Shi, X. / Liu, L. / Zhao, J. / Wang, X. / Zhang, Z. / Zhang, L.
History
DepositionApr 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 19, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Mar 10, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name
Revision 1.5Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Spike protein S1
L: antibody light chain
H: antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6314
Polymers71,4103
Non-polymers2211
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-26 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.230, 90.150, 112.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein / SARS-CoV-2 receptor binding domain


Mass: 24600.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2
#2: Antibody antibody light chain / Immunoglobulin light chain


Mass: 22686.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#3: Antibody antibody heavy chain / Immunoglobulin heavy chain


Mass: 24122.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated 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
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium formate dihydrate, 0.1M sodium acetate trihydrate, pH 4.0, 18% PEG 5000 mme

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.85→90.15 Å / Num. obs: 17230 / % possible obs: 99.9 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 14.3
Reflection shellResolution: 2.85→2.92 Å / Rmerge(I) obs: 1.452 / Num. unique obs: 1273

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 2.85→59.552 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 855 4.96 %
Rwork0.2191 16372 -
obs0.2214 17227 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.89 Å2 / Biso mean: 74.4316 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.85→59.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4806 0 0 0 4806
Num. residues----636
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.85-3.02860.35641380.30852693
3.0286-3.26240.31221240.29262692
3.2624-3.59070.34261400.26652702
3.5907-4.11020.30861490.22252706
4.1102-5.17790.21171370.1772735
5.1779-59.5520.22821670.19582844
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)
14.4139-1.7553-0.84343.16731.27993.9483-0.0511-0.34470.58350.02990.1659-0.1605-0.4043-0.4204-0.11710.6012-0.0226-0.0630.5442-0.0730.4807-14.6078-10.719826.0189
21.5057-1.00711.22027.04034.93325.10640.1140.1074-0.0539-0.0294-0.14160.15620.064-0.06430.00110.4005-0.03330.03890.36330.02780.3294-2.9089-36.33782.581
35.2474-3.36183.06825.583-1.80555.4962-0.0621-0.0188-0.36330.2368-0.00010.39550.35440.37580.14750.44720.00520.04120.4094-0.04230.357510.4997-65.48113.3385
47.227-2.2501-1.18617.1464-1.22364.26860.1104-0.01640.3056-0.05230.1381-0.75290.12830.5379-0.28290.4035-0.0143-0.01670.3811-0.15280.53317.8495-30.39473.905
510.04773.33950.94164.1521-0.78154.34750.09590.93870.1234-0.5349-0.2050.03120.0167-0.02470.11260.44010.10510.02950.49780.0030.361522.0553-66.9226-7.5328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain EE333 - 601
2X-RAY DIFFRACTION2chain H and resid 1:127H1 - 127
3X-RAY DIFFRACTION3chain H and resid 128:229H128 - 229
4X-RAY DIFFRACTION4chain L and resid 1:111L1 - 111
5X-RAY DIFFRACTION5chain L and resid 112:213L112 - 213

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