7K43

SARS-CoV-2 spike in complex with the S2M11 neutralizing antibody Fab fragment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms.

Tortorici, M.A.Beltramello, M.Lempp, F.A.Pinto, D.Dang, H.V.Rosen, L.E.McCallum, M.Bowen, J.Minola, A.Jaconi, S.Zatta, F.De Marco, A.Guarino, B.Bianchi, S.Lauron, E.J.Tucker, H.Zhou, J.Peter, A.Havenar-Daughton, C.Wojcechowskyj, J.A.Case, J.B.Chen, R.E.Kaiser, H.Montiel-Ruiz, M.Meury, M.Czudnochowski, N.Spreafico, R.Dillen, J.Ng, C.Sprugasci, N.Culap, K.Benigni, F.Abdelnabi, R.Foo, S.C.Schmid, M.A.Cameroni, E.Riva, A.Gabrieli, A.Galli, M.Pizzuto, M.S.Neyts, J.Diamond, M.S.Virgin, H.W.Snell, G.Corti, D.Fink, K.Veesler, D.

(2020) Science 370: 950-957

  • DOI: https://doi.org/10.1126/science.abe3354
  • Primary Citation of Related Structures:  
    7K3Q, 7K43, 7K45, 7K4N

  • PubMed Abstract: 

    Efficient therapeutic options are needed to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has caused more than 922,000 fatalities as of 13 September 2020. We report the isolation and characterization of two ultrapotent SARS-CoV-2 human neutralizing antibodies (S2E12 and S2M11) that protect hamsters against SARS-CoV-2 challenge. Cryo-electron microscopy structures show that S2E12 and S2M11 competitively block angiotensin-converting enzyme 2 (ACE2) attachment and that S2M11 also locks the spike in a closed conformation by recognition of a quaternary epitope spanning two adjacent receptor-binding domains. Antibody cocktails that include S2M11, S2E12, or the previously identified S309 antibody broadly neutralize a panel of circulating SARS-CoV-2 isolates and activate effector functions. Our results pave the way to implement antibody cocktails for prophylaxis or therapy, circumventing or limiting the emergence of viral escape mutants.


  • 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,
D [auth B],
G [auth E]
1,281Severe 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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S2M11 Fab fragment (heavy chain)B [auth H],
E [auth C],
H [auth F]
125Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
S2M11 Fab fragment (light chain)C [auth L],
F [auth D],
I [auth G]
108Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
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-glucopyranoseL [auth K],
S,
Z
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
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 
AB [auth E]
BB [auth E]
CB [auth E]
DB [auth E]
EA [auth A]
AB [auth E],
BB [auth E],
CB [auth E],
DB [auth E],
EA [auth A],
EB [auth E],
FA [auth A],
FB [auth E],
GA [auth A],
GB [auth E],
HA [auth A],
HB [auth E],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth B],
PA [auth B],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth B],
UA [auth B],
VA [auth B],
WA [auth B],
XA [auth B],
YA [auth E],
ZA [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

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)R01GM120553

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2021-01-27
    Changes: Structure summary