7P8J | pdb_00007p8j

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 2

• PDB DOI: https://doi.org/10.2210/pdb7P8J/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): Italian Association for Cancer Research, Italian Ministry of Education, Other private, Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 6.58 Å
• R-Value Free: 
  0.345 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.318 (Depositor), 0.320 (DCC) 
• R-Value Observed: 
  0.320 (Depositor) 

Starting Model: experimental

Literature

Constrained Evolution of SARS-CoV-2 Spike in Rhinolophus affinis Bats

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: 196.77 kDa 
• Atom Count: 13,136 
• Modelled Residue Count: 1,580 
• 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 EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: Q9BYF1-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B, D	233	Bat coronavirus RaTG13	Mutation(s): 0
Glycosylation
Glycosylation Sites: 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	E, H, J, M	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, K, L, N	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 6.58 Å
• R-Value Free:  0.345 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.318 (Depositor), 0.320 (DCC) 
• R-Value Observed: 0.320 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.9	α = 90
b = 107.717	β = 90
c = 251.754	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
Italian Association for Cancer Research	Italy	MFAG 20075
Italian Ministry of Education	Italy	PRIN 2017 2017RPHBCW_001
Italian Ministry of Education	Italy	Department of Excellence 2018-2022
Other private	United States	Giovanni Armenise-Harvard Foundation Career Development Award CDA2013
Other private	Switzerland	Velux Stiftung Opthalmology Grant id. 1375
Other private	Japan	Mizutani Foundation For Glycoscience Grant id. 200039
Other government	Belgium	NATO Science for Peace and Security Program Grant id. G5701

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
• Version 1.3: 2024-11-13
  Changes: Structure summary