8UZF

Crystal structure of chimeric RaTG13 RBD complexed with chimeric mouse ACE2

PDB DOI: https://doi.org/10.2210/pdb8UZF/pdb

Classification: VIRAL PROTEIN/HYDROLASE
Organism(s): Mus musculus, Bat coronavirus RaTG13
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2023-11-15 Released: 2024-07-24
Deposition Author(s): Zhang, W., Shi, K., Aihara, H., Li, F.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.28 Å
R-Value Free: 0.280
R-Value Work: 0.223
R-Value Observed: 0.226

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of chimeric RaTG13 RBD complexed with chimeric mouse ACE2

Zhang, W., Shi, K., Aihara, H., Li, F.

To be published.

Macromolecule Content

Total Structure Weight: 189.63 kDa
Atom Count: 12,858
Modelled Residue Count: 1,563
Deposited Residue Count: 1,628
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A, B	597	Mus musculus	Mutation(s): 0 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
Find proteins for Q8R0I0 (Mus musculus) Explore Q8R0I0 Go to UniProtKB: Q8R0I0
IMPC: MGI:1917258
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q9BYF1Q8R0I0
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q8R0I0-1Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor binding domain	C [auth E], D [auth F]	217	Bat coronavirus RaTG13	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D [auth F]
Sequence Annotations Expand
Reference Sequence

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 [auth C], F [auth D]	2		N-Glycosylation	Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]
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	G	3		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain R [auth F] SDF format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth B]	K [auth A], Q [auth B], R [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth F] Interactions & Density Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth F]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	H [auth A], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	J [auth A], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B]	I [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain M [auth B] Interactions & Density Focus chain I [auth A] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.28 Å
R-Value Free: 0.280
R-Value Work: 0.223
R-Value Observed: 0.226
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.556	α = 90
b = 119.004	β = 95.92
c = 109.075	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
STARANISO	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI089728
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI110700
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047

Revision History (Full details and data files)

Version 1.0: 2024-07-24
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

8UZF

Crystal structure of chimeric RaTG13 RBD complexed with chimeric mouse ACE2

Crystal structure of chimeric RaTG13 RBD complexed with chimeric mouse ACE2

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)