7F5R

Crystal structure of SARS-CoV-2 Y453F-RBD bound to mink ACE2

• PDB DOI: https://doi.org/10.2210/pdb7F5R/pdb

• Classification: VIRAL PROTEIN/PROTEIN BINDING
• Organism(s): Neogale vison, Severe acute respiratory syndrome coronavirus 2
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2021-06-22 Released: 2022-06-22 
• Deposition Author(s): Wang, X.Q., Ding, Q., Lan, J., Ren, W.L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.218 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 Y453F-RBD bound to mink ACE2

Wang, X.Q., Ding, Q., Lan, J., Ren, W.L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 278.02 kDa 
• Atom Count: 19,386 
• Modelled Residue Count: 2,357 
• Deposited Residue Count: 2,382 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mink ACE2	A, C [auth B], E [auth D]	597	Neogale vison	Mutation(s): 0  EC: 3.4
UniProt
Find proteins for A0A8C7BTF2 (Neovison vison) Explore A0A8C7BTF2  Go to UniProtKB:  A0A8C7BTF2
Glycosylation
Glycosylation Sites: 3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B [auth E], D [auth C], F	197	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  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	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], K [auth E], L [auth B], M [auth B], N [auth B], O [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 0.218 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 290.185	α = 90
b = 130.185	β = 90
c = 136.887	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Wang, X.Q., Ding, Q., Lan, J., Ren, W.L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary