7KQB | pdb_00007kqb

SARS-CoV-2 spike glycoprotein:Fab 5A6 complex I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7KQB

This is version 1.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7M71

Literature

Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia.

Asarnow, D.Wang, B.Lee, W.H.Hu, Y.Huang, C.W.Faust, B.Ng, P.M.L.Ngoh, E.Z.X.Bohn, M.Bulkley, D.Pizzorno, A.Ary, B.Tan, H.C.Lee, C.Y.Minhat, R.A.Terrier, O.Soh, M.K.Teo, F.J.Yeap, Y.Y.C.Seah, S.G.K.Chan, C.E.Z.Connelly, E.Young, N.J.Maurer-Stroh, S.Renia, L.Hanson, B.J.Rosa-Calatrava, M.Manglik, A.Cheng, Y.Craik, C.S.Wang, C.I.

(2021) Cell 184: 3192-3204.e16

  • DOI: https://doi.org/10.1016/j.cell.2021.04.033
  • Primary Citation Related Structures: 
    7KQB, 7KQE, 7M71, 7M7B

  • PubMed Abstract: 

    Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by binding of the viral Spike protein to host receptor angiotensin-converting enzyme 2 (ACE2), followed by fusion of viral and host membranes. Although antibodies that block this interaction are in emergency use as early coronavirus disease 2019 (COVID-19) therapies, the precise determinants of neutralization potency remain unknown. We discovered a series of antibodies that potently block ACE2 binding but exhibit divergent neutralization efficacy against the live virus. Strikingly, these neutralizing antibodies can inhibit or enhance Spike-mediated membrane fusion and formation of syncytia, which are associated with chronic tissue damage in individuals with COVID-19. As revealed by cryoelectron microscopy, multiple structures of Spike-antibody complexes have distinct binding modes that not only block ACE2 binding but also alter the Spike protein conformational cycle triggered by ACE2 binding. We show that stabilization of different Spike conformations leads to modulation of Spike-mediated membrane fusion with profound implications for COVID-19 pathology and immunity.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, University of California, San Francisco (UCSF) School of Medicine, San Francisco, CA, USA; QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 551.08 kDa 
  • Atom Count: 32,215 
  • Modeled Residue Count: 4,105 
  • Deposited Residue Count: 4,950 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,208Severe 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
Glycosylation
Glycosylation Sites: 8Go to GlyGen: P0DTC2-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 5A6 heavy chainD [auth H],
F [auth K]
449Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 5A6 light chainE [auth L],
G [auth J]
214Homo sapiensMutation(s): 0 

Small Molecules

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

Query on NAG



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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.15.0
MODEL REFINEMENTISOLDE1.0

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)United StatesP50AI150476
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD020054
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD021741

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Refinement description, Structure summary