7S0C | pdb_00007s0c

Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody N-612-017


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7S0C

This is version 1.3 of the entry. See complete history

Literature

Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display.

Tanaka, S.Olson, C.A.Barnes, C.O.Higashide, W.Gonzalez, M.Taft, J.Richardson, A.Martin-Fernandez, M.Bogunovic, D.Gnanapragasam, P.N.P.Bjorkman, P.J.Spilman, P.Niazi, K.Rabizadeh, S.Soon-Shiong, P.

(2022) Cell Rep 38: 110348-110348

  • DOI: https://doi.org/10.1016/j.celrep.2022.110348
  • Primary Citation Related Structures: 
    7S0B, 7S0C, 7S0D, 7S0E

  • PubMed Abstract: 

    The increasing prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with the ability to escape existing humoral protection conferred by previous infection and/or immunization necessitates the discovery of broadly reactive neutralizing antibodies (nAbs). Utilizing mRNA display, we identify a set of antibodies against SARS-CoV-2 spike (S) proteins and characterize the structures of nAbs that recognize epitopes in the S1 subunit of the S glycoprotein. These structural studies reveal distinct binding modes for several antibodies, including the targeting of rare cryptic epitopes in the receptor-binding domain (RBD) of S that interact with angiotensin-converting enzyme 2 (ACE2) to initiate infection, as well as the S1 subdomain 1. Further, we engineer a potent ACE2-blocking nAb to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. We demonstrate that mRNA display is an approach for the rapid identification of nAbs that can be used in combination to combat emerging SARS-CoV-2 variants.


  • Organizational Affiliation
    • ImmunityBio, Inc., 9920 Jefferson Boulevard, Culver City, CA 90232, USA.

Macromolecule Content 

  • Total Structure Weight: 525.95 kDa 
  • Atom Count: 29,598 
  • Modeled Residue Count: 3,818 
  • Deposited Residue Count: 4,701 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoproteinA [auth B],
B [auth A],
C
1,271Severe acute respiratory syndrome coronavirus 2Mutation(s): 6 
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: 12Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
N-612-017 Fab Heavy ChainD [auth H],
F [auth M]
230Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
N-612-017 Light ChainE [auth L],
G [auth N]
214Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD 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]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth A],
BA [auth A],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth A],
Y [auth A],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3.1

Structure Validation

View Full Validation Report



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

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2025-05-28
    Changes: Data collection