6ZDH

SARS-CoV-2 Spike glycoprotein in complex with a neutralizing antibody EY6A Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.4 of the entry. See complete history


Literature

Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient.

Zhou, D.Duyvesteyn, H.M.E.Chen, C.P.Huang, C.G.Chen, T.H.Shih, S.R.Lin, Y.C.Cheng, C.Y.Cheng, S.H.Huang, Y.C.Lin, T.Y.Ma, C.Huo, J.Carrique, L.Malinauskas, T.Ruza, R.R.Shah, P.N.M.Tan, T.K.Rijal, P.Donat, R.F.Godwin, K.Buttigieg, K.R.Tree, J.A.Radecke, J.Paterson, N.G.Supasa, P.Mongkolsapaya, J.Screaton, G.R.Carroll, M.W.Gilbert-Jaramillo, J.Knight, M.L.James, W.Owens, R.J.Naismith, J.H.Townsend, A.R.Fry, E.E.Zhao, Y.Ren, J.Stuart, D.I.Huang, K.A.

(2020) Nat Struct Mol Biol 27: 950-958

  • DOI: 10.1038/s41594-020-0480-y
  • Primary Citation of Related Structures:  
    6ZCZ, 6ZDG, 6ZDH, 6ZER, 6ZFO

  • PubMed Abstract: 
  • The COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID-19 and have shown that it neutralizes SARS-CoV-2 and cross-reacts with SARS-CoV-1 ...

    The COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID-19 and have shown that it neutralizes SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds the receptor binding domain (RBD) of the viral spike glycoprotein tightly (K D of 2 nM), and a 2.6-Å-resolution crystal structure of an RBD-EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues within this footprint are key to stabilizing the pre-fusion spike. Cryo-EM analyses of the pre-fusion spike incubated with EY6A Fab reveal a complex of the intact spike trimer with three Fabs bound and two further multimeric forms comprising the destabilized spike attached to Fab. EY6A binds what is probably a major neutralizing epitope, making it a candidate therapeutic for COVID-19.


    Organizational Affiliation

    Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan. arthur1726@cgmh.org.tw.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinA, B, C1288Severe acute respiratory syndrome coronavirus 2Mutation(s): 5 
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EY6A heavy chainF [auth D],
H [auth G],
D [auth H]
226Homo sapiensMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
EY6A light chainG [auth F],
I,
E [auth L]
215Homo sapiensMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J [auth E],
K [auth J],
L [auth K],
M,
N,
J [auth E],
K [auth J],
L [auth K],
M,
N,
O,
P,
Q,
R,
S,
T,
U,
V
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth B],
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth C],
NA [auth C],
OA [auth C],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N00065X/1
Wellcome TrustUnited Kingdom101122/Z/13/Z
CAMS Innovation Fund for Medical Sciences (CIFMS)China2018-I2M-2-002

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-08-12
    Changes: Database references, Structure summary
  • Version 2.2: 2020-10-21
    Changes: Database references
  • Version 2.3: 2021-02-10
    Changes: Database references
  • Version 2.4: 2021-12-22
    Changes: Database references