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

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Basic information

Entry
Database: PDB / ID: 7beh
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-316 Fab
Components
  • COVOX-316 heavy chain
  • COVOX-316 light chain
  • Spike glycoproteinSpike protein
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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: 2.3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Spike glycoprotein
H: COVOX-316 heavy chain
L: COVOX-316 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4839
Polymers72,9143
Non-polymers1,5706
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-2 kcal/mol
Surface area28080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.020, 150.860, 46.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody COVOX-316 heavy chain


Mass: 25640.928 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 COVOX-316 light chain


Mass: 24121.697 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, 3 molecules E

#1: Protein Spike glycoprotein / Spike protein / 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 104 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 0.1 M bis-Tris pH 5.5 and 25 % (w/v) PEG 3350

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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: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→52 Å / Num. obs: 28312 / % possible obs: 85.7 % / Redundancy: 11 % / Biso Wilson estimate: 50.88 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.032 / Net I/σ(I): 14.2
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 633 / CC1/2: 0.223

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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: 2.3→45.27 Å / SU ML: 0.3266 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.3519
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2296 1392 4.93 %
Rwork0.2132 26846 -
obs0.214 28238 85.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 104 100 4964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254989
X-RAY DIFFRACTIONf_angle_d0.52316796
X-RAY DIFFRACTIONf_chiral_restr0.0442763
X-RAY DIFFRACTIONf_plane_restr0.0041862
X-RAY DIFFRACTIONf_dihedral_angle_d14.20571779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.3674780.37381289X-RAY DIFFRACTION42.56
2.38-2.480.3478900.33821712X-RAY DIFFRACTION55.28
2.48-2.590.34511120.30612141X-RAY DIFFRACTION69.37
2.59-2.730.30681330.29472694X-RAY DIFFRACTION86.4
2.73-2.90.31021390.27483080X-RAY DIFFRACTION98.44
2.9-3.120.28831560.25793089X-RAY DIFFRACTION99.97
3.12-3.440.25151580.24223155X-RAY DIFFRACTION99.97
3.44-3.930.22371700.20353156X-RAY DIFFRACTION100
3.93-4.950.19621760.16253187X-RAY DIFFRACTION100
4.95-45.270.181800.183343X-RAY DIFFRACTION99.86
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)
17.639462442342.0469006355-0.711198848463.177317564290.1694764012794.88492720476-0.02302865131440.4180498854240.247253707641-0.171835081736-0.00362980977166-0.214851320238-0.004691825239380.579918590606-0.09639265430990.3733160998430.04422809658270.0566503647650.5004226355590.00967068509620.40577704338713.621351347837.1602519437-4.22066023971
29.1373594842.487081617730.4208875885523.832067854690.3616649312483.11754785874-0.253937038251.656161410651.81454802701-1.269295071050.8065225406560.174770291827-0.4657929283050.254765892887-0.02748461423120.730639223573-0.1223597573520.09805228869010.6860175679340.172912082040.7183870549043.0801911856144.902108354-11.0644996071
30.340309581886-0.0586800641071.2554404583.913880572361.762894516119.08720023267-0.3937182779690.5359227311461.004945299110.273238168326-0.8763612591770.30123276334-2.197462550150.7396246553781.184216551011.02927237763-0.1721990854390.1711040495330.7989445815970.1375679499212.139174648459.6382693737454.1575039976-5.4177304925
43.184835785041.25012357812-0.337948365422.43963197064-1.391554942944.397367749060.230997131619-0.06975833368280.1923532999490.262356710983-0.06979332993290.1120731065270.01823759269920.0622471535803-0.2302103163860.3264886445560.04176924545930.01434497735460.2993513837150.003597429086060.447197427647-0.89203982540533.38495735551.24536716131
54.574418882994.57013757772-1.905590095899.38277755086-3.816122317731.885231371510.527189978769-0.6883219376410.3456413834210.745720081863-0.6336898743040.171290514615-0.5613503207050.5500975896730.1437301284360.432148400432-0.0209832646807-0.02188949640960.390129329389-0.04572798560430.389068832098-1.6037913053123.640518745916.405979314
65.672753268222.835672099841.690054403056.035315375512.020377502052.985885947940.1752615457790.0104742594019-0.3589172225820.103202739208-0.2302806599810.05504453770130.552281613632-0.217874580293-0.04336320370760.4334682523670.0525820838894-0.005714817545270.3629563286770.05775327211270.361410520464-1.829696512131.2727794276-5.40092047881
77.56778959766-2.020680355460.000909670281736.58155458299-3.558108924292.141061906730.553731630871-0.2173101568521.19958546471.00959430246-0.943452677467-1.38255756104-1.335272432321.697522484410.05035668457971.44766673581-0.438958091214-0.2075265043651.244548641910.3173346305721.4063125720518.562181766153.05763288411.05746670141
82.266444838010.7719890796110.3755281651375.963161145860.5103745597451.75436832762-0.09551105761340.2355600253030.132853603518-0.7328808606070.01877214125180.204466371359-0.02808002542510.00118128453559-0.01661241238030.390662460633-0.00997417670205-0.05689328450550.3507025485470.0313688743570.430346396667-13.76824191420.8318661608273.63730103631
94.332852078812.213973613040.4031981715896.945114926210.2230706544731.9674820211-0.01720011839210.00989464558873-0.151585006616-0.129730087539-0.04441574096820.01895959817430.2877329724290.004535723739460.01063056330190.3956027134380.01886894419060.06332531331220.365728453432-0.01743617978880.386052036293-8.993929419243.6750042664314.1112794876
102.321494774530.8338025335280.3791952798815.429832937450.4469062459431.883613905390.03340183847080.0872602715092-0.156436029625-0.000986301764396-0.07235990337960.360825934918-0.099152861437-0.0452818085760.01177320150340.3151521106770.00463656430264-0.006811655869280.353091569534-0.02064048871310.338926463032-11.70802588342.43615593047.81661050235
112.235481833320.992616890626-0.7816548157873.59842104789-0.953024488460.412910422484-0.161110805714-0.0938571613173-0.3732425512990.144177054587-0.096935515164-0.169358938383-0.01693574561880.1093475717320.229916349440.374721671489-0.0119503174971-0.01351399270950.407776270003-0.01500442244820.424496416515-28.7322352204-27.986948279813.0380855414
127.195609759710.414295448194-2.66283409064.311077627940.2630420369637.325909939460.1359842107220.00406676881982-0.2034941912830.3030609432820.05228624551560.7536185046320.397614336678-1.13173681029-0.001528686213380.350897336139-0.0397450990202-0.07569551077960.50724204413-0.02356559787630.485589131359-37.6958499564-35.067172998615.1283186694
136.336834088980.1944657850321.835114230756.059951704360.4705945403270.599728063174-0.626809391839-0.200196619389-0.63111803816-0.01960205343620.226472476885-0.06139618041360.9267108459870.5289899197640.01593559901930.57492058468-0.0295079874084-0.04853103716130.3592614740470.06000682763230.704316497097-31.5713907473-40.458056730416.0361138132
142.691996178942.208977850760.3272630359192.3563932241-0.536895119781.27601559504-0.0787971051934-0.1750932752160.3348010955690.0739644879718-0.03513367487470.78811891317-0.085630000353-0.2026035561630.0895476793660.4018945552740.09486411793270.04849624909790.386612103949-0.03463516619870.683091520385-30.9629501385.8445791806618.6413402224
156.86046366728-2.862693769762.034551496688.18259498856-1.684018479143.12706147358-0.308879555941-0.4403683462070.2905789518620.5780886194830.2007119292240.02217059149720.0134203077204-0.04165229862550.1425889873930.38429498828-0.02069924736860.03309177651730.457834104788-0.08399772440770.485099767133-30.7983871198-21.191515526326.172647594
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 333 through 364 )EA333 - 3641 - 32
22chain 'E' and (resid 365 through 380 )EA365 - 38033 - 48
33chain 'E' and (resid 381 through 393 )EA381 - 39349 - 61
44chain 'E' and (resid 394 through 459 )EA394 - 45962 - 127
55chain 'E' and (resid 460 through 494 )EA460 - 494128 - 162
66chain 'E' and (resid 495 through 516 )EA495 - 516163 - 184
77chain 'E' and (resid 517 through 527 )EA517 - 527185 - 195
88chain 'H' and (resid 1 through 44 )HF1 - 441 - 44
99chain 'H' and (resid 45 through 64 )HF45 - 6445 - 64
1010chain 'H' and (resid 65 through 115 )HF65 - 11565 - 115
1111chain 'H' and (resid 116 through 186 )HF116 - 186116 - 181
1212chain 'H' and (resid 187 through 212 )HF187 - 212182 - 209
1313chain 'H' and (resid 213 through 224 )HF213 - 224210 - 221
1414chain 'L' and (resid 2 through 117 )LL2 - 1171 - 116
1515chain 'L' and (resid 118 through 213 )LL118 - 213117 - 212

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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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