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- PDB-9jr5: Crystal structure of PCoV-GD receptor-binding domain complexed wi... -

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Basic information

Entry
Database: PDB / ID: 9jr5
TitleCrystal structure of PCoV-GD receptor-binding domain complexed with squirrel ACE2
Components
  • Angiotensin-converting enzyme
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / PCoV-GD / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / cell surface / extracellular space / metal ion binding / identical protein binding / membrane / 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. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesPangolin coronavirus
Petaurus norfolcensis (squirrel glider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.414 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
Revision 1.1Aug 13, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 15, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,2796
Polymers90,6232
Non-polymers1,6574
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)195.143, 195.143, 145.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 20927.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pangolin coronavirus / Gene: S / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A7D6TQ96
#2: Protein Angiotensin-converting enzyme


Mass: 69695.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petaurus norfolcensis (squirrel glider)
Gene: ACE2 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: A0A8D2KIZ1, Hydrolases; Acting on peptide bonds (peptidases)
#3: 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.: 2
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
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 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.: 1 / 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
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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium chloride hexahydrate, 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: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.41→50 Å / Num. obs: 19205 / % possible obs: 98.94 % / Redundancy: 24.5 % / CC1/2: 0.989 / Net I/σ(I): 8.25
Reflection shellResolution: 3.41→3.54 Å / Num. unique obs: 1830 / CC1/2: 0.762

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 3.414→48.786 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2821 960 5.01 %
Rwork0.2185 --
obs0.2217 19166 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.414→48.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6305 0 103 0 6408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0266623
X-RAY DIFFRACTIONf_angle_d1.5539005
X-RAY DIFFRACTIONf_dihedral_angle_d19.4843902
X-RAY DIFFRACTIONf_chiral_restr0.071963
X-RAY DIFFRACTIONf_plane_restr0.0091152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4145-3.59440.37411420.31612456X-RAY DIFFRACTION96
3.5944-3.81950.35971570.28592571X-RAY DIFFRACTION100
3.8195-4.11430.25731460.23622583X-RAY DIFFRACTION100
4.1143-4.52810.2691110.20192612X-RAY DIFFRACTION100
4.5281-5.18270.27841220.18482646X-RAY DIFFRACTION100
5.1827-6.52710.30241350.22132639X-RAY DIFFRACTION100
6.5271-48.7860.23951470.19022699X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.09040.1014-0.08010.0972-0.03520.02160.65860.02520.3846-0.8623-1.13170.12380.125-0.09750.00171.12790.05450.02810.8314-0.19990.903326.137-32.79325.899
20.10130.4503-0.14831.1702-0.48481.04050.3285-0.787-0.17370.24670.09450.9352-0.2114-0.54040.08440.7975-0.0671-0.10050.8720.21741.347621.43-30.91134.773
30.0527-0.02550.00740.0295-0.08040.1188-0.4465-0.3229-1.42350.944-0.5622-1.22731.75440.2169-0.03341.2968-0.30020.28260.9370.07251.815436.217-39.53332.961
41.00330.1023-0.1630.3842-0.10280.18240.3911-0.901-0.30860.93-0.54190.92090.657-0.3714-0.00061.46450.07850.49821.08950.49932.687332.892-45.41341.725
50.708-0.77690.06821.2713-0.97121.0357-0.156-0.11430.079-0.1768-0.1323-0.32910.22570.0306-00.7306-0.07520.10870.65930.02370.62131.166-21.90535.311
60.35260.0619-0.22371.7758-0.81630.5393-0.80750.8086-1.48271.33220.25731.3639-0.20060.4999-0.05020.83180.07880.11930.8084-0.00031.091721.706-20.43542.867
70.78390.5658-0.72840.7036-0.15370.51770.04590.10090.376-0.0333-0.01570.0956-0.06570.0085-0.00020.70310.05380.00230.77970.06480.66827.274-12.6834.432
81.2447-0.7601-0.06050.8811-0.41940.5738-0.33680.5134-0.28010.1058-0.14530.49380.51720.2047-0.01190.6401-0.03790.04160.7107-0.01710.551935.838-1.83830.465
91.2659-0.25721.27870.0103-0.46240.6425-0.09270.20570.7088-0.10860.08550.00930.1472-0.14720.00160.81220.1295-0.010.98960.04840.786437.63610.79726.302
101.6786-1.05891.42360.5737-0.66221.3168-0.2210.4375-0.312-0.1355-0.42990.2102-0.20720.0794-0.00150.8664-0.2744-0.12971.30410.24231.084557.48424.0668.871
110.40870.1402-0.27691.2055-0.70511.5423-0.0616-0.26620.14030.1926-0.16250.2182-0.18-0.20260.00070.601-0.00570.06830.7165-0.05160.906263.15617.83933.28
121.7632-1.1339-0.33941.44760.5363-0.2626-0.15620.1885-0.4151-0.3860.3966-0.40710.01510.19150.00390.6519-0.15150.06050.84390.07110.697176.72815.58613.562
131.48910.90641.37711.23450.54991.70380.05530.5173-0.1166-0.0406-0.41710.11980.1516-0.3266-0.00430.63140.12490.17610.6104-0.09470.864159.103-11.76915.387
141.19020.2387-0.00391.2445-0.11980.2728-0.02840.02770.37490.1639-0.1364-0.24430.00820.0096-0.0010.65860.00170.04730.58360.0220.494761.828-5.75224.056
152.0861.7610.00521.15990.10351.009-0.20220.31321.2082-0.0146-0.02660.0848-0.21540.1960.00010.61710.0015-0.01460.69790.11520.700263.74123.08722.285
161.0187-0.1074-0.33870.438-0.62310.67830.25380.268-0.0303-0.2179-0.10890.25880.24360.0858-0.00010.66540.01940.12440.70230.0980.609570.502-0.34932.973
170.12490.45050.05361.2195-0.5701-0.3365-0.0481-0.630.1292-0.0767-0.1919-0.57370.10670.3346-0.07610.6753-0.06660.14180.7363-0.02740.563870.7476.83234.982
182.01092.01541.99912.02221.99752.0020.2145-0.44491.16-0.0795-0.0219-0.2446-0.2161-0.149-0.21961.96820.0415-0.08140.9395-0.38433.778474.1936.78520.351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND RESID 337:349 )E337 - 349
2X-RAY DIFFRACTION2( CHAIN E AND RESID 350:360 )E350 - 360
3X-RAY DIFFRACTION3( CHAIN E AND RESID 361:380 )E361 - 380
4X-RAY DIFFRACTION4( CHAIN E AND RESID 381:393 )E381 - 393
5X-RAY DIFFRACTION5( CHAIN E AND RESID 394:459 )E394 - 459
6X-RAY DIFFRACTION6( CHAIN E AND RESID 460:469 )E460 - 469
7X-RAY DIFFRACTION7( CHAIN E AND RESID 470:517 )E470 - 517
8X-RAY DIFFRACTION8( CHAIN A AND RESID 18:52 )A18 - 52
9X-RAY DIFFRACTION9( CHAIN A AND RESID 53:128 )A53 - 128
10X-RAY DIFFRACTION10( CHAIN A AND RESID 129:193 )A129 - 193
11X-RAY DIFFRACTION11( CHAIN A AND RESID 194:251 )A194 - 251
12X-RAY DIFFRACTION12( CHAIN A AND RESID 252:293 )A252 - 293
13X-RAY DIFFRACTION13( CHAIN A AND RESID 294:350 )A294 - 350
14X-RAY DIFFRACTION14( CHAIN A AND RESID 351:431 )A351 - 431
15X-RAY DIFFRACTION15( CHAIN A AND RESID 432:513 )A432 - 513
16X-RAY DIFFRACTION16( CHAIN A AND RESID 514:547 )A514 - 547
17X-RAY DIFFRACTION17( CHAIN A AND RESID 548:608 )A548 - 608
18X-RAY DIFFRACTION18( CHAIN A AND RESID 616:616 )A616

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