7FAT

Structure Determination of the RBD-NB1A7

• PDB DOI: https://doi.org/10.2210/pdb7FAT/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Camelus bactrianus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-07 Released: 2022-05-18 
• Deposition Author(s): Geng, Y., Shi, Z.Z., Li, X.Y., Wang, L., Sun, Z.C., Zhang, H.W., Chen, X.C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.242 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Structural basis of nanobodies neutralizing SARS-CoV-2 variants

Shi, Z., Li, X., Wang, L., Sun, Z., Zhang, H., Chen, X., Cui, Q., Qiao, H., Lan, Z., Zhang, X., Li, X., Li, L., Xu, J., Gong, R., Fan, C., Geng, Y.

(2022) Structure 30: 707

• DOI: https://doi.org/10.1016/j.str.2022.02.011

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

Macromolecule Content

• Total Structure Weight: 39.85 kDa 
• Atom Count: 2,711 
• Modelled Residue Count: 316 
• Deposited Residue Count: 357 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	219	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nb_1A7	B	138	Camelus bactrianus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.242 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.663	α = 90
b = 183.795	β = 90
c = 42.209	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-18 
Deposition Author(s): Geng, Y., Shi, Z.Z., Li, X.Y., Wang, L., Sun, Z.C., Zhang, H.W., Chen, X.C.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31670743

Revision History  

• Version 1.0: 2022-05-18
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary