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- PDB-7bz5: Structure of COVID-19 virus spike receptor-binding domain complex... -

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Basic information

Entry
Database: PDB / ID: 7bz5
TitleStructure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody
Components
  • Heavy chain of B38
  • Light chain of B38
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / covid-19 antibody / VIRAL PROTEIN / 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 / membrane fusion / entry receptor-mediated virion attachment to host cell / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsWu, Y. / Qi, J. / Gao, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31872745, 81902058 China
CitationJournal: Science / Year: 2020
Title: A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2.
Authors: Wu, Y. / Wang, F. / Shen, C. / Peng, W. / Li, D. / Zhao, C. / Li, Z. / Li, S. / Bi, Y. / Yang, Y. / Gong, Y. / Xiao, H. / Fan, Z. / Tan, S. / Wu, G. / Tan, W. / Lu, X. / Fan, C. / Wang, Q. / ...Authors: Wu, Y. / Wang, F. / Shen, C. / Peng, W. / Li, D. / Zhao, C. / Li, Z. / Li, S. / Bi, Y. / Yang, Y. / Gong, Y. / Xiao, H. / Fan, Z. / Tan, S. / Wu, G. / Tan, W. / Lu, X. / Fan, C. / Wang, Q. / Liu, Y. / Zhang, C. / Qi, J. / Gao, G.F. / Gao, F. / Liu, L.
History
DepositionApr 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 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 1.4Mar 10, 2021Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
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
Revision 1.6Oct 30, 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
H: Heavy chain of B38
L: Light chain of B38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3604
Polymers73,1393
Non-polymers2211
Water9,350519
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-15 kcal/mol
Surface area27970 Å2
Unit cell
Length a, b, c (Å)195.226, 86.417, 56.827
Angle α, β, γ (deg.)90.000, 100.190, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 25951.219 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 Heavy chain of B38


Mass: 23442.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Light chain of B38


Mass: 23745.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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


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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
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: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.15 M ammonium sulfate, 0.1 M MES pH 6, 15% w/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97981 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97981 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 80095 / % possible obs: 99.41 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.11 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.044 / Net I/σ(I): 16.9
Reflection shellResolution: 1.84→1.92 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7992 / CC1/2: 0.662 / Rpim(I) all: 0.526

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG, 4TSA

6lzg

4tsa


Resolution: 1.84→28.49 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.88
RfactorNum. reflection% reflection
Rfree0.1914 2000 2.5 %
Rwork0.1671 --
obs0.1677 80064 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 161.9 Å2 / Biso mean: 39.9588 Å2 / Biso min: 17.27 Å2
Refinement stepCycle: final / Resolution: 1.84→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 14 519 5345
Biso mean--80.18 45.16 -
Num. residues----628
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.880.34191260.2924926505289
1.88-1.940.27871430.24455965739100
1.94-1.990.24731430.209255755718100
1.99-2.060.22091440.195956315775100
2.06-2.130.22311440.188456025746100
2.13-2.220.21191440.183356055749100
2.22-2.320.17671430.176555885731100
2.32-2.440.20181440.179556135757100
2.44-2.590.23851440.179756415785100
2.59-2.790.20551430.182556195762100
2.79-3.070.22871450.178156245769100
3.07-3.510.1791450.167656445789100
3.51-4.430.17381440.13856765820100
4.43-28.490.14481480.140557245872100
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)
11.8723-0.0539-0.27942.60280.49992.0675-0.0548-0.03020.16540.0528-0.06780.5655-0.2185-0.42950.06240.22290.02980.01210.2291-0.00150.3029-72.7298-29.796611.4994
22.25590.7956-0.3440.789-0.07730.4041-0.04640.1468-0.1178-0.02760.0686-0.09510.06550.0861-0.02720.2417-0.0051-0.00490.1972-0.03330.1557-30.9878-29.3986-11.5244
31.70180.7451-0.77781.1866-0.59681.0630.0237-0.11360.08120.06120.01080.02250.04470.0103-0.02680.23440.0036-0.02360.2512-0.03140.2069-25.9253-19.71762.509
Refinement TLS group
IDEnd auth seq-IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1619X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain HH0 - 217
3X-RAY DIFFRACTION3chain LL0 - 215

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