7L2C

Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite.

Cerutti, G.Guo, Y.Zhou, T.Gorman, J.Lee, M.Rapp, M.Reddem, E.R.Yu, J.Bahna, F.Bimela, J.Huang, Y.Katsamba, P.S.Liu, L.Nair, M.S.Rawi, R.Olia, A.S.Wang, P.Zhang, B.Chuang, G.Y.Ho, D.D.Sheng, Z.Kwong, P.D.Shapiro, L.

(2021) Cell Host Microbe 29: 819

  • DOI: https://doi.org/10.1016/j.chom.2021.03.005
  • Primary Citation of Related Structures:  
    7L2C, 7L2D, 7L2E, 7L2F, 7LQW

  • PubMed Abstract: 

    Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. Here, we report cryo-EM and crystal structures for seven potent NTD-directed neutralizing antibodies in complex with spike or isolated NTD. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed that all seven antibodies target a common surface, bordered by glycans N17, N74, N122, and N149. This site-formed primarily by a mobile β-hairpin and several flexible loops-was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD-directed neutralizing antibodies appear to target a single supersite.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B
342Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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: 7Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
2-51 heavy chainC [auth H],
E [auth C]
227Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
2-51 light chainD [auth L],
F [auth D]
215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth E]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
H [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
Y [auth B],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE (Subject of Investigation/LOI)
Query on PGE

Download Ideal Coordinates CCD File 
KB [auth C]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CAC (Subject of Investigation/LOI)
Query on CAC

Download Ideal Coordinates CCD File 
X [auth A]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
ACT (Subject of Investigation/LOI)
Query on ACT

Download Ideal Coordinates CCD File 
KA [auth B]
LA [auth B]
RB [auth D]
TA [auth H]
U [auth A]
KA [auth B],
LA [auth B],
RB [auth D],
TA [auth H],
U [auth A],
UA [auth H],
V [auth A],
W [auth A],
YA [auth L]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
AB [auth C]
BB [auth C]
CB [auth C]
DB [auth C]
EA [auth B]
AB [auth C],
BB [auth C],
CB [auth C],
DB [auth C],
EA [auth B],
EB [auth C],
FA [auth B],
FB [auth C],
GA [auth B],
GB [auth C],
HA [auth B],
HB [auth C],
IA [auth B],
IB [auth C],
JA [auth B],
JB [auth C],
LB [auth D],
MA [auth H],
MB [auth D],
NA [auth H],
NB [auth D],
O [auth A],
OA [auth H],
OB [auth D],
P [auth A],
PA [auth H],
PB [auth D],
Q [auth A],
QA [auth H],
QB [auth D],
R [auth A],
RA [auth H],
S [auth A],
SA [auth H],
T [auth A],
VA [auth L],
WA [auth L],
XA [auth L],
ZA [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.791α = 90
b = 115.785β = 99.97
c = 137.606γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateChinaJack Ma Foundation

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 1.2: 2021-04-14
    Changes: Database references
  • Version 1.3: 2021-05-26
    Changes: Database references
  • Version 1.4: 2023-10-18
    Changes: Data collection, Database references, Refinement description