7K8Z

Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C135

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.

Barnes, C.O., Jette, C.A., Abernathy, M.E., Dam, K.A., Esswein, S.R., Gristick, H.B., Malyutin, A.G., Sharaf, N.G., Huey-Tubman, K.E., Lee, Y.E., Robbiani, D.F., Nussenzweig, M.C., West Jr., A.P., Bjorkman, P.J.

(2020) Nature 588: 682-687

  • DOI: https://doi.org/10.1038/s41586-020-2852-1
  • Primary Citation of Related Structures:  
    7K8M, 7K8N, 7K8O, 7K8P, 7K8Q, 7K8R, 7K8S, 7K8T, 7K8U, 7K8V, 7K8W, 7K8X, 7K8Y, 7K8Z, 7K90

  • PubMed Abstract: 

    • The coronavirus disease 2019 (COVID-19) pandemic presents an urgent health crisis. Human neutralizing antibodies that target the host ACE2 receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein 1-5 show promise therapeutically and are being evaluated clinically 6-8 ...

    The coronavirus disease 2019 (COVID-19) pandemic presents an urgent health crisis. Human neutralizing antibodies that target the host ACE2 receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein 1-5 show promise therapeutically and are being evaluated clinically 6-8 . Here, to identify the structural correlates of SARS-CoV-2 neutralization, we solved eight new structures of distinct COVID-19 human neutralizing antibodies 5 in complex with the SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed us to classify the antibodies into categories: (1) neutralizing antibodies encoded by the VH3-53 gene segment with short CDRH3 loops that block ACE2 and bind only to 'up' RBDs; (2) ACE2-blocking neutralizing antibodies that bind both up and 'down' RBDs and can contact adjacent RBDs; (3) neutralizing antibodies that bind outside the ACE2 site and recognize both up and down RBDs; and (4) previously described antibodies that do not block ACE2 and bind only to up RBDs 9 . Class 2 contained four neutralizing antibodies with epitopes that bridged RBDs, including a VH3-53 antibody that used a long CDRH3 with a hydrophobic tip to bridge between adjacent down RBDs, thereby locking the spike into a closed conformation. Epitope and paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 to escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects and suggesting combinations for clinical use, and provide insight into immune responses against SARS-CoV-2.

    Organizational Affiliation: 

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. bjorkman@caltech.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,259Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S, 2
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
C135 Fab Heavy ChainD [auth H],
F [auth M]		231Homo sapiensMutation(s): 0 
Entity Groups  
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
C135 Fab Light ChainE [auth L],
G [auth N]		214Homo 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
H [auth D],
I [auth E],
J [auth F],
K [auth G],
L [auth I],
H [auth D],
I [auth E],
J [auth F],
K [auth G],
L [auth I],
M [auth J],
O,
P,
Q,
R,
S,
T,
U
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-glucopyranoseN [auth K]6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G82348BZ
GlyCosmos:  G82348BZ
GlyGen:  G82348BZ
Entity ID: 6
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-glucopyranose
V
4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth C]
BA [auth A]
BB [auth C]
CA [auth A]
AA [auth A],
AB [auth C],
BA [auth A],
BB [auth C],
CA [auth A],
CB [auth C],
DA [auth A],
EA [auth A],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B],
NA [auth B],
OA [auth B],
PA [auth B],
QA [auth B],
RA [auth B],
SA [auth C],
TA [auth C],
UA [auth C],
VA [auth C],
W [auth A],
WA [auth C],
X [auth A],
XA [auth C],
Y [auth A],
YA [auth C],
Z [auth A],
ZA [auth C]
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: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17
RECONSTRUCTIONcryoSPARC2.15

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01-AI138938-S1
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP50-AI150464-13

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references