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- PDB-9jr4: Crystal structure of RaTG13 receptor-binding domain complexed wit... -

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Basic information

Entry
Database: PDB / ID: 9jr4
TitleCrystal structure of RaTG13 receptor-binding domain complexed with squirrel ACE2
Components
  • Angiotensin-converting enzyme
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / RaTG13 / receptor-binding domain / squirrel ACE2
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / transporter activator activity / angiotensin maturation / metallocarboxypeptidase activity ...Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / transporter activator activity / angiotensin maturation / metallocarboxypeptidase activity / positive regulation of cardiac muscle contraction / brush border membrane / virus receptor activity / endopeptidase activity / entry receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / cell surface / extracellular space / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile.
Similarity search - Domain/homology
Angiotensin-converting enzyme
Similarity search - Component
Biological speciesPetaurus norfolcensis (squirrel glider)
Bat coronavirus RaTG13
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsLan, J. / Nan, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Cross-species recognition of squirrel ACE2 by the receptor binding domains of SARS-CoV-2, RaTG13, PCoV-GD and PCoV-GX
Authors: Wang, C. / Nan, X. / Deng, Y. / Fan, S. / Lan, J.
History
DepositionSep 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Angiotensin-converting enzyme
E: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,23310
Polymers91,9282
Non-polymers2,3058
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.990, 168.990, 86.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules BE

#1: Protein Angiotensin-converting enzyme


Mass: 69598.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Petaurus norfolcensis is not available during the biocuration, replaced by A0A8D2KIZ1 temporarily.
Source: (gene. exp.) Petaurus norfolcensis (squirrel glider)
Gene: ACE2 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: A0A8D2KIZ1, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Spike glycoprotein


Mass: 22330.055 Da / Num. of mol.: 1 / Fragment: receptor-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat coronavirus RaTG13 / Production host: Trichoplusia ni (cabbage looper)

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Sugars , 3 types, 6 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 18 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 8% v/v Tacsimate pH8.0, 20% w/v Polyethylene glycol 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 32541 / % possible obs: 99.29 % / Redundancy: 27.6 % / CC1/2: 0.999 / Net I/σ(I): 16.1
Reflection shellResolution: 2.76→2.86 Å / Num. unique obs: 3200 / CC1/2: 0.906

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 2.76→28.22 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2781 1604 4.96 %
Rwork0.211 --
obs0.2142 32367 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.76→28.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6395 0 146 16 6557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096718
X-RAY DIFFRACTIONf_angle_d1.0659119
X-RAY DIFFRACTIONf_dihedral_angle_d24.0662477
X-RAY DIFFRACTIONf_chiral_restr0.057983
X-RAY DIFFRACTIONf_plane_restr0.0061164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.850.44591560.35972716X-RAY DIFFRACTION99
2.85-2.950.38251320.3262746X-RAY DIFFRACTION99
2.95-3.070.39691380.29712733X-RAY DIFFRACTION99
3.07-3.210.33421400.27932754X-RAY DIFFRACTION99
3.21-3.380.36511440.27392762X-RAY DIFFRACTION99
3.38-3.590.35111560.24072785X-RAY DIFFRACTION99
3.59-3.860.28121590.21522746X-RAY DIFFRACTION100
3.86-4.250.26211470.19792804X-RAY DIFFRACTION100
4.25-4.860.25291410.17522836X-RAY DIFFRACTION100
4.87-6.120.25341400.18572879X-RAY DIFFRACTION100
6.12-28.220.20611510.17493002X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -50.8676 Å / Origin y: -0.5559 Å / Origin z: -32.1085 Å
111213212223313233
T0.8446 Å2-0.0013 Å20.0474 Å2-0.7538 Å20.0157 Å2--0.8195 Å2
L0.0961 °20.1907 °20.0225 °2-1.4507 °2-0.8678 °2--0.5057 °2
S-0.0594 Å °-0.0277 Å °-0.0233 Å °0.1602 Å °-0.005 Å °-0.1202 Å °0.027 Å °0.2486 Å °0.0298 Å °
Refinement TLS groupSelection details: all

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