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: 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 ...

    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. dveesler@uw.edu katja.fink@alumni.ethz.ch.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinA,
D [auth B],
G [auth E]
1281Severe 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
S2M11 Fab fragment (heavy chain)E [auth C],
H [auth F],
B [auth H]
125Homo 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
S2M11 Fab fragment (light chain)F [auth D],
I [auth G],
C [auth L]
108Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
J [auth I],
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
J [auth I],
K [auth J],
M,
N,
O,
P,
Q,
R,
T,
U,
V,
W,
X,
Y
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D 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 Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 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)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