7LY2

SARS-CoV-2 S/S2M11/S2M28 Global Refinement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2.

McCallum, M.De Marco, A.Lempp, F.A.Tortorici, M.A.Pinto, D.Walls, A.C.Beltramello, M.Chen, A.Liu, Z.Zatta, F.Zepeda, S.di Iulio, J.Bowen, J.E.Montiel-Ruiz, M.Zhou, J.Rosen, L.E.Bianchi, S.Guarino, B.Fregni, C.S.Abdelnabi, R.Foo, S.C.Rothlauf, P.W.Bloyet, L.M.Benigni, F.Cameroni, E.Neyts, J.Riva, A.Snell, G.Telenti, A.Whelan, S.P.J.Virgin, H.W.Corti, D.Pizzuto, M.S.Veesler, D.

(2021) Cell 184: 2332

  • DOI: https://doi.org/10.1016/j.cell.2021.03.028
  • Primary Citation of Related Structures:  
    7LXW, 7LXX, 7LXY, 7LXZ, 7LY0, 7LY2, 7LY3

  • PubMed Abstract: 

    The SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite (designated site i) recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge, albeit selecting escape mutants in some animals. Indeed, several SARS-CoV-2 variants, including the B.1.1.7, B.1.351, and P.1 lineages, harbor frequent mutations within the NTD supersite, suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs for protective immunity and vaccine design.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinA,
F [auth B],
K [auth J]
1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 9 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 18Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S2M11 Fab Light Chain variable regionB [auth D],
G [auth C],
L [auth K]
104Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
S2M11 Fab Heavy Chain variable regionC [auth E],
H [auth F],
M
122Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
S2M28 Fab Heavy Chain variable regionD [auth H],
I [auth G],
N
117Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
S2M28 Fab Light Chain variable regionE [auth L],
J [auth I],
O
106Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
P, S, V
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Q, R, T, U, W
Q, R, T, U, W, X
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
BA [auth A]
BB [auth B]
CA [auth A]
AA [auth A],
AB [auth B],
BA [auth A],
BB [auth B],
CA [auth A],
CB [auth J],
DA [auth A],
DB [auth J],
EA [auth A],
EB [auth J],
FA [auth A],
FB [auth J],
GA [auth A],
GB [auth J],
HA [auth A],
HB [auth J],
IA [auth A],
IB [auth J],
JA [auth A],
JB [auth J],
KA [auth A],
KB [auth J],
LA [auth A],
LB [auth J],
MA [auth A],
MB [auth J],
NA [auth B],
NB [auth J],
OA [auth B],
OB [auth J],
PA [auth B],
PB [auth J],
QA [auth B],
QB [auth J],
RA [auth B],
SA [auth B],
TA [auth B],
UA [auth B],
VA [auth B],
WA [auth B],
XA [auth B],
Y [auth A],
YA [auth B],
Z [auth A],
ZA [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM120553

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Database references