7P8I

Receptor-binding domain (RBD) of the spike protein of the bat coronavirus RaTG13 virus in complex with the extracellular domain of human angiotensin-converting enzyme 2 (ACE2) - Crystal form 1

• PDB DOI: https://doi.org/10.2210/pdb7P8I/pdb

• Classification: CELL INVASION
• Organism(s): Homo sapiens, Bat coronavirus RaTG13
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-07-22 Released: 2022-08-03 
• Deposition Author(s): Scietti, L., Castelli, M., Faravelli, S., Clementi, N., Mancini, N., Forneris, F.
• Funding Organization(s): The Giovanni Armenise-Harvard Foundation, Italian Association for Cancer Research, Mizutani Foundation for Glycoscience, NATO Science for Peace and Security Program, Velux Stiftung, Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.50 Å
• R-Value Free: 0.294 
• R-Value Work: 0.278 
• R-Value Observed: 0.279 

Literature

Evidence of SARS-CoV-2 Direct Evolution in R. affinis Bats Driven by Affinity and Dynamics Optimization of the Spike Protein

Castelli, M., Scietti, L., Faravelli, S., Clementi, N., Forneris, F., Mancini, N.

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: surface plasmon resonance

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 196.26 kDa 
• Atom Count: 13,101 
• Modelled Residue Count: 1,579 
• Deposited Residue Count: 1,670 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A, C	602	Homo sapiens	Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B, D	233	Bat coronavirus RaTG13	Mutation(s): 0
UniProt
Find proteins for A0A6B9WHD3 (Bat coronavirus RaTG13) Explore A0A6B9WHD3  Go to UniProtKB:  A0A6B9WHD3

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	E, H, J, K	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, I, L	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	M [auth C], N [auth D], 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: 4.50 Å
• R-Value Free: 0.294 
• R-Value Work: 0.278 
• R-Value Observed: 0.279 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.557	α = 90
b = 131.214	β = 99.77
c = 115.725	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-03 
Deposition Author(s): Scietti, L., Castelli, M., Faravelli, S., Clementi, N., Mancini, N., Forneris, F.

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Funding Organization	Location	Grant Number
The Giovanni Armenise-Harvard Foundation	United States	CDA2013
Italian Association for Cancer Research	Italy	MFAG 20075
Mizutani Foundation for Glycoscience	Japan	200039
NATO Science for Peace and Security Program	Belgium	SPS.MYP G5701
Velux Stiftung	Switzerland	1375
Italian Ministry of Education	Italy	PRIN 2017 2017RPHBCW_001
Italian Ministry of Education	Italy	Department of Excellence 2018-2022

Revision History  

• Version 1.0: 2022-08-03
  Type: Initial release
  
• Version 1.1: 2023-08-16
  Changes: Data collection
• Version 1.2: 2024-01-31
  Changes: Refinement description