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Structure paper

TitleThe antigenic anatomy of SARS-CoV-2 receptor binding domain.
Journal, issue, pagesCell, Vol. 184, Issue 8, Page 2183-2200.e22, Year 2021
Publish dateApr 15, 2021
AuthorsWanwisa 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 /
PubMed AbstractAntibodies 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.
External linksCell / PubMed:33756110 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.04 - 7.3 Å
Structure data

12274

7nd3

EMDB-12274, PDB-7nd3:
EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-40 Fab
Method: EM (single particle) / Resolution: 3.7 Å

12275

7nd4

EMDB-12275, PDB-7nd4:
EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-88 Fab
Method: EM (single particle) / Resolution: 3.6 Å

12276

7nd5

EMDB-12276, PDB-7nd5:
EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-150 Fab
Method: EM (single particle) / Resolution: 3.4 Å

12277

7nd6

EMDB-12277, PDB-7nd6:
EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-40 Fab
Method: EM (single particle) / Resolution: 7.3 Å

12278

7nd7

EMDB-12278, PDB-7nd7:
EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-316 Fab
Method: EM (single particle) / Resolution: 3.6 Å

12279

7nd8

EMDB-12279, PDB-7nd8:
EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-384 Fab
Method: EM (single particle) / Resolution: 3.5 Å

12280

7nd9

EMDB-12280, PDB-7nd9:
EM structure of SARS-CoV-2 Spike glycoprotein (one RBD up) in complex with COVOX-253H55L Fab
Method: EM (single particle) / Resolution: 2.8 Å

12281

7nda

EMDB-12281, PDB-7nda:
EM structure of SARS-CoV-2 Spike glycoprotein (all RBD down) in complex with COVOX-253H55L Fab
Method: EM (single particle) / Resolution: 3.3 Å

12282

7ndb

EMDB-12282, PDB-7ndb:
EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-253H165L Fab
Method: EM (single particle) / Resolution: 4.6 Å

12283

7ndc

EMDB-12283, PDB-7ndc:
EM structure of SARS-CoV-2 Spike glycoprotein (all RBD down) in complex with COVOX-159
Method: EM (single particle) / Resolution: 4.1 Å

12284

7ndd

EMDB-12284, PDB-7ndd:
EM structure of SARS-CoV-2 Spike glycoprotein (one RBD up) in complex with COVOX-159
Method: EM (single particle) / Resolution: 4.2 Å

PDB-7beh:
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-316 Fab
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-7bei:
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-150 Fab
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-7bej:
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 1)
Method: X-RAY DIFFRACTION / Resolution: 2.42 Å

PDB-7bek:
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 2)
Method: X-RAY DIFFRACTION / Resolution: 2.04 Å

PDB-7bel:
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-88 and COVOX-45 Fabs
Method: X-RAY DIFFRACTION / Resolution: 2.53 Å

PDB-7bem:
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 scFv
Method: X-RAY DIFFRACTION / Resolution: 2.52 Å

PDB-7ben:
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253 and COVOX-75 Fabs
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-7beo:
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253H55L and COVOX-75 Fabs
Method: X-RAY DIFFRACTION / Resolution: 3.19 Å

PDB-7bep:
Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-384 and S309 Fabs
Method: X-RAY DIFFRACTION / Resolution: 2.61 Å

Chemicals

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM / Tris

ChemComp-HOH:
WATER / Water

ChemComp-NO3:
NITRATE ION / Nitrate

ChemComp-CL:
Unknown entry / Chloride

ChemComp-FMT:
FORMIC ACID / Formic acid

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-ACT:
ACETATE ION / Acetate

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-PRO:
PROLINE / Proline

ChemComp-IMD:
IMIDAZOLE / Imidazole

ChemComp-BR:
BROMIDE ION / Bromide

ChemComp-PG6:
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol

ChemComp-IOD:
IODIDE ION / Iodide

ChemComp-GLU:
GLUTAMIC ACID / Glutamic acid

ChemComp-GLY:
GLYCINE / Glycine

ChemComp-PGE:
TRIETHYLENE GLYCOL / Polyethylene glycol

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
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

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