8BE1 | pdb_00008be1

SARS-CoV-2 RBD in complex with a Fab fragment of a neutralising antibody mRBD2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.284 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.249 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8BE1

This is version 1.3 of the entry. See complete history

Literature

Rapid discovery of monoclonal antibodies by microfluidics-enabled FACS of single pathogen-specific antibody-secreting cells.

Fischer, K.Lulla, A.So, T.Y.Pereyra-Gerber, P.Raybould, M.I.J.Kohler, T.N.Yam-Puc, J.C.Kaminski, T.S.Hughes, R.Pyeatt, G.L.Leiss-Maier, F.Brear, P.Matheson, N.J.Deane, C.M.Hyvonen, M.Thaventhiran, J.E.D.Hollfelder, F.

(2025) Nat Biotechnol 43: 960-970

  • DOI: https://doi.org/10.1038/s41587-024-02346-5
  • Primary Citation Related Structures: 
    8BE1

  • PubMed Abstract: 

    Monoclonal antibodies are increasingly used to prevent and treat viral infections and are pivotal in pandemic response efforts. Antibody-secreting cells (ASCs; plasma cells and plasmablasts) are an excellent source of high-affinity antibodies with therapeutic potential. Current methods to study antigen-specific ASCs either have low throughput, require expensive and labor-intensive screening or are technically demanding and therefore not widely accessible. Here we present a straightforward technology for the rapid discovery of monoclonal antibodies from ASCs. Our approach combines microfluidic encapsulation of single cells into an antibody capture hydrogel with antigen bait sorting by conventional flow cytometry. With our technology, we screened millions of mouse and human ASCs and obtained monoclonal antibodies against severe acute respiratory syndrome coronavirus 2 with high affinity (<1 pM) and neutralizing capacity (<100 ng ml -1 ) in 2 weeks with a high hit rate (>85% of characterized antibodies bound the target). By facilitating access to the underexplored ASC compartment, the approach enables efficient antibody discovery and immunological studies into the generation of protective antibodies.


  • Organizational Affiliation
    • Department of Biochemistry, University of Cambridge, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 143.3 kDa 
  • Atom Count: 9,866 
  • Modeled Residue Count: 1,221 
  • Deposited Residue Count: 1,286 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody heavy chain
A, D
230Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody light chain
B, E
215Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S1
C, F
198Severe 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
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth B]
J [auth B]
K [auth C]
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth C],
L [auth C],
M [auth D],
N [auth D],
O [auth D],
P [auth D],
Q [auth D],
R [auth E],
S [auth E],
T [auth E],
U [auth F],
V [auth F],
W [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.284 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.47α = 90
b = 194.62β = 97.16
c = 62.09γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary
  • Version 1.3: 2026-05-13
    Changes: Database references