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

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYF1
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain C	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B, D	233	Bat coronavirus RaTG13	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	Interactions Focus chain E Focus chain H Focus chain J Focus chain K
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	Interactions Focus chain F Focus chain G Focus chain I Focus chain L
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C]	M [auth C], N [auth D], O [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D]

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-03

Deposition Author(s):

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