8BEC | pdb_00008bec

Crystal structure of the SARS-CoV-2 S RBD in complex with pT1375 scFV

• PDB DOI: https://doi.org/10.2210/pdb8BEC/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2022-10-21 Released: 2023-11-01 
• Deposition Author(s): Hansen, G., Ssebyatika, G.L., Krey, T.
• Funding Organization(s): Other government, German Federal Ministry for Education and Research, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Models: experimental

Literature

Activity of broadly neutralizing antibodies against sarbecoviruses: a trade-off between SARS-CoV-2 variants and distant coronaviruses?

Stein, C.S., Hansen, G., Ssebyatika, G.L., Stroeh, L., Benecke, T., Menz, S., Waldmann, J.-Y., Vollmer, B., Tipp, S., Ochulor, O., Herold, E., Schwarzloh, B., Mutschall, D., Zischke, J.-Y., Cordes, A., Puppe, W., Schneider, T., Hinrichs, I., Blasczyk, R., Kleine-Weber, H., Hoffmann, M., Hoeper, M., Kaiser, F.K., Gonzalez-Hernandez, M., Armando, F.K., Ciurkiewicz, M., Beythien, G., Poehlmann, S., Baumgaertner, W., Gruenewald, K., Osterhaus, A., Schulz, T., Krey, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 99.41 kDa 
• Atom Count: 7,121 
• Modeled Residue Count: 838 
• Deposited Residue Count: 900 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pT1375 single-chain Fv	A, C	251	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B, D	199	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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-glucopyranose	F	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.446	α = 90
b = 91.559	β = 90
c = 156.704	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-01 
Deposition Author(s): Hansen, G., Ssebyatika, G.L., Krey, T.

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Funding Organization	Location	Grant Number
Other government		14-76103-184 CORONA-12/20
Other government	Germany	14-76103-184 CORONA-15/20
German Federal Ministry for Education and Research	Germany	COVIM (FKZ: 01KX2021)
German Federal Ministry for Education and Research	Germany	RAPID (FKZ: 01KI1723G)
German Research Foundation (DFG)	Germany	EXC 2155
German Research Foundation (DFG)	Germany	2485 VIPER (398066876/GRK 2485/1)

Revision History  

• Version 1.0: 2023-11-01
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description