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- PDB-7bej: Crystal structure of the receptor binding domain of SARS-CoV-2 Sp... -

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Basic information

Entry
Database: PDB / ID: 7bej
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 1)
Components
  • COVOX-158 heavy chain
  • COVOX-158 light chain
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody / germline / V-gene / receptor-binding-domain / spike / neutralisation / protection / glycosylation / valency / VIRAL PROTEIN / IMMUNE SYSTEM / 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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 / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 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 / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
FORMIC ACID / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsZhou, D. / Zhao, Y. / Ren, J. / Stuart, D.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 China
CitationJournal: Cell / Year: 2021
Title: The antigenic anatomy of SARS-CoV-2 receptor binding domain.
Authors: Wanwisa Dejnirattisai / Daming Zhou / Helen M Ginn / Helen M E Duyvesteyn / Piyada Supasa / James Brett Case / Yuguang Zhao / Thomas S Walter / Alexander J Mentzer / Chang Liu / Beibei Wang ...Authors: Wanwisa Dejnirattisai / Daming Zhou / Helen M Ginn / Helen M E Duyvesteyn / Piyada Supasa / James Brett Case / Yuguang Zhao / Thomas S Walter / Alexander J Mentzer / Chang Liu / Beibei Wang / Guido C Paesen / Jose Slon-Campos / César López-Camacho / Natasha M Kafai / Adam L Bailey / Rita E Chen / Baoling Ying / Craig Thompson / Jai Bolton / Alex Fyfe / Sunetra Gupta / Tiong Kit Tan / Javier Gilbert-Jaramillo / William James / Michael Knight / Miles W Carroll / Donal Skelly / Christina Dold / Yanchun Peng / Robert Levin / Tao Dong / Andrew J Pollard / Julian C Knight / Paul Klenerman / Nigel Temperton / David R Hall / Mark A Williams / Neil G Paterson / Felicity K R Bertram / C Alistair Siebert / Daniel K Clare / Andrew Howe / Julika Radecke / Yun Song / Alain R Townsend / Kuan-Ying A Huang / Elizabeth E Fry / Juthathip Mongkolsapaya / Michael S Diamond / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and ...Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC < 0.1 μg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.
History
DepositionDec 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: 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 1.4Oct 23, 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
H: COVOX-158 heavy chain
L: COVOX-158 light chain
E: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,98412
Polymers69,9533
Non-polymers1,0319
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-11 kcal/mol
Surface area27320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.172, 232.320, 135.162
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

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody COVOX-158 heavy chain


Mass: 23402.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody COVOX-158 light chain


Mass: 23400.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules E

#3: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 23150.891 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: Homo sapiens (human) / References: UniProt: P0DTC2
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 55 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: containing 3.5 M NaCOOH pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.42→53.4 Å / Num. obs: 32012 / % possible obs: 98.5 % / Redundancy: 23.7 % / Biso Wilson estimate: 53.43 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.051 / Net I/σ(I): 7.6
Reflection shellResolution: 2.42→2.46 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1343 / CC1/2: 0.363

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Processing

Software
NameVersionClassification
GDA1.18.1_3865data collection
PHENIX1.18.1_3865refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZCZ

6zcz


Resolution: 2.42→53.36 Å / SU ML: 0.3922 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.8342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2314 1610 5.08 %
Rwork0.1896 30108 -
obs0.1918 31718 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.5 Å2
Refinement stepCycle: LAST / Resolution: 2.42→53.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 68 47 4889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274959
X-RAY DIFFRACTIONf_angle_d0.61286733
X-RAY DIFFRACTIONf_chiral_restr0.0446758
X-RAY DIFFRACTIONf_plane_restr0.0038860
X-RAY DIFFRACTIONf_dihedral_angle_d17.34961778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.490.4091960.34942004X-RAY DIFFRACTION79.76
2.49-2.570.34071290.30332309X-RAY DIFFRACTION91.45
2.57-2.660.32761510.27122523X-RAY DIFFRACTION99.41
2.66-2.770.30171420.25322533X-RAY DIFFRACTION99.96
2.77-2.90.28771180.24282551X-RAY DIFFRACTION99.96
2.9-3.050.31031350.21572555X-RAY DIFFRACTION100
3.05-3.240.25831250.20192558X-RAY DIFFRACTION100
3.24-3.490.22481310.19672564X-RAY DIFFRACTION100
3.49-3.840.23851570.18192575X-RAY DIFFRACTION100
3.84-4.40.19881330.14652596X-RAY DIFFRACTION100
4.4-5.540.16521440.1422597X-RAY DIFFRACTION99.96
5.54-53.360.21461490.18582743X-RAY DIFFRACTION99.83
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)
11.222104477052.85920083032-0.4759421961467.24600610107-0.7556605794143.689015014570.289672048521-0.370835904235-0.1661469905210.97612140076-0.182856924333-0.239002763894-0.7042663015940.447648410578-0.08760622903540.5451452048-0.1069811344610.002992464491060.4971919107090.01920616210620.31460823322830.808779303793.53246592947.48507129285
22.55753666392.9049787529-1.624188304634.585221935-1.530747742431.548971549620.119120092686-0.355343587955-0.1043661787120.625647457859-0.30836075974-0.520164466636-0.3370373242040.3709525924630.2316239719140.428186501402-0.0644555081198-0.1049589591640.4660311943950.05069051076020.40390663686329.109653603981.77657171847.72873124648
32.445065679762.87028113079-1.422144946064.63767323705-1.404570083031.399592788640.160232879372-0.56098983731-0.0341005869960.270449924085-0.453210325263-0.339788270484-0.4475916771880.3279543868810.1001538714410.554855710094-0.0772865198881-0.06854937574860.4620127042830.02675441672440.44878658674128.990839787386.02326483935.69082650344
43.138295726432.67195536664-1.707112889655.54250044173-1.593774145850.9500181640670.3831024596860.008718168026520.1729297525270.615649888851-0.355897997836-0.0216525807684-0.6646008931790.336043004578-0.1877051411540.481787212256-0.01712858872070.03379017577330.460652551503-0.1757016948210.45294498098540.4675576352110.489019947-7.80152572867
51.423419931330.1460932327290.2991517385312.20051135416-0.9855965720674.161768851240.114907483984-0.04035716714090.005225837237260.140481301103-0.08633361284310.187020028345-0.095126951996-0.302407319824-0.001029562893070.486645469189-0.0229770508462-0.01135622905950.427778837702-0.07326333436930.49534465634434.2056684382109.862184263-10.7485976532
64.11798381256-0.4888803766971.84259779692.270343504271.389154704072.010235243750.5059473300870.06151051289010.3966809064290.135652664083-0.3415336199330.630964691614-0.642741076638-0.1613830261530.194613805460.677063915251-0.0543668772241-0.004688752922680.45564041726-0.09627395011420.48048719922533.5860541608118.385564766-6.93068433632
70.591866293643-0.0509929076173-1.000322054384.571924376-2.39130172914.032889494580.05296887002840.0215361973615-0.0513004494423-0.0814205905194-0.02644312108950.2697969607230.0592351463945-0.270595039868-0.08379671977760.348167640803-0.043341825112-0.05695686741020.4208364208560.01446210153980.41956143604425.219107205477.7995177742-15.4272407917
80.318999928720.3658149765320.1198087293312.476707155660.1203224790320.548578551334-0.000561848987695-0.1105784359850.0618934958948-0.0879592616333-0.0124520583519-0.278580097435-0.1794738678610.2564283848860.03895372148090.395778553258-0.05167973147130.003691211267350.545200000586-0.03386383173070.43506363133241.1190272306100.613525487-19.1796212114
93.708923753011.940470034631.684213434664.148423721162.196943291653.12755134574-0.1560274425340.2879132198930.125341934285-0.3757491573720.13474498728-0.45107172649-0.3209433930060.4401302563170.01391761967890.445041663816-0.04036906963430.03279251689570.4465891734640.0371200036090.43200065529244.5881382038109.713907131-24.1284045494
101.56369967606-1.220473017031.202609195134.11159488843-2.248253130613.710443370150.0989189215081-0.0618795649151-0.353503187204-0.136981893850.1646059979650.1677205830280.358078491246-0.165807772833-0.2340368884870.487520297167-0.0052559352753-0.03207950699440.5083586828890.01165619731580.51682482665717.818645889842.891691075814.4448874872
111.365167127860.9464082454730.6465013693442.68431629176-3.429297649297.711285598310.127670497212-0.1062440954930.0329190251427-0.174492421037-0.0344012606649-0.4298769076620.7893955772120.9186889082510.06440081966750.4595065961050.094453431506-0.01415056892120.5922688189180.08308063542550.48955009961331.993183474442.271606490317.5798156746
124.70314739040.2715877152030.2110573179726.436704601010.292255906874.21640033825-0.05911590119890.001548490005410.09569762182590.1791892254150.0665652799977-0.111217418119-0.243013277278-0.06562204498460.1018732972370.322443069868-0.00214440605631-0.06373589974390.450755331928-0.003093942362020.39552333718323.70886708754.380639355510.8923132678
131.6999364298-0.837773275596-0.3064491955243.3605143536-0.6630938326160.4289716070070.05834837891790.00601332788809-0.05313679518410.126233680839-0.05012052020050.0385984342646-0.128672441641-0.1295864296650.01021101003760.320390037265-0.0227926242273-0.02103159860020.4559298267510.004175741233460.33505144595818.5434360661.31739812727.64543863338
140.4083088502120.535970573808-0.7304077321192.054867209511.707228208038.671153074660.0787335243813-0.427919792808-0.428001037820.6935377295930.310637965891-0.7942190054780.2933935941610.884958469886-0.09428960681850.6568161698070.118264425782-0.08075936882830.843426932237-0.03709606367840.58575496265323.029677148340.217888902930.4854853761
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 17 )HA1 - 171 - 17
22chain 'H' and (resid 18 through 72 )HA18 - 7218 - 72
33chain 'H' and (resid 73 through 113 )HA73 - 11373 - 113
44chain 'H' and (resid 114 through 138 )HA114 - 138114 - 135
55chain 'H' and (resid 139 through 207 )HA139 - 207136 - 206
66chain 'H' and (resid 208 through 218 )HA208 - 218207 - 217
77chain 'L' and (resid 1 through 90 )LC1 - 901 - 90
88chain 'L' and (resid 91 through 163 )LC91 - 16391 - 165
99chain 'L' and (resid 164 through 213 )LC164 - 213166 - 217
1010chain 'E' and (resid 333 through 364 )EE333 - 3641 - 32
1111chain 'E' and (resid 365 through 393 )EE365 - 39333 - 61
1212chain 'E' and (resid 394 through 409 )EE394 - 40962 - 77
1313chain 'E' and (resid 410 through 516 )EE410 - 51678 - 184
1414chain 'E' and (resid 517 through 527 )EE517 - 527185 - 195

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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