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

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Basic information

Entry
Database: PDB / ID: 9jtd
TitleCrystal structure of PCoV-GD receptor binding domain complexed with fox ACE2
Components
  • Angiotensin-converting enzyme
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / PCoV-GD / receptor binding domain / fox 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 / regulation of cardiac conduction / peptidyl-dipeptidase activity / transporter activator activity / carboxypeptidase activity / brush border membrane / metallopeptidase 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 / regulation of cardiac conduction / peptidyl-dipeptidase activity / transporter activator activity / carboxypeptidase activity / brush border membrane / metallopeptidase activity / virus receptor activity / endopeptidase activity / entry receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / cell surface / proteolysis / 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 speciesVulpes vulpes (red fox)
Pangolin coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsJun, L. / Xiaoyan, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of PCoV-GD receptor binding domain complexed with fox ACE2
Authors: Jun, L. / Xiaoyan, N.
History
DepositionOct 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,0845
Polymers90,6902
Non-polymers1,3943
Water00
1
A: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3304
Polymers68,9351
Non-polymers1,3943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)21,7541
Polymers21,7541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint17 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.952, 193.952, 151.024
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 Angiotensin-converting enzyme


Mass: 68935.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vulpes vulpes (red fox) / Gene: ACE2 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: A0A3Q7RAT9, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Spike glycoprotein / PCoV-GD / S glycoprotein / E2 / Peplomer protein


Mass: 21754.266 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: A0A7D6PMV8
#3: 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.: 2 / Source method: obtained synthetically
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
#4: 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: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium chloride, 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: BL02U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.59→50 Å / Num. obs: 16994 / % possible obs: 99.11 % / Redundancy: 23.6 % / CC1/2: 1 / Net I/σ(I): 9.67
Reflection shellResolution: 3.59→3.72 Å / Num. unique obs: 1632 / CC1/2: 0.685

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 3.59→33.07 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2628 850 5 %
Rwork0.2289 --
obs0.2306 16994 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.59→33.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6479 0 0 0 6479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056662
X-RAY DIFFRACTIONf_angle_d0.729056
X-RAY DIFFRACTIONf_dihedral_angle_d4.846910
X-RAY DIFFRACTIONf_chiral_restr0.045965
X-RAY DIFFRACTIONf_plane_restr0.0061162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.59-3.810.31311390.30252585X-RAY DIFFRACTION97
3.81-4.10.28771450.24992666X-RAY DIFFRACTION100
4.11-4.520.23081180.23052700X-RAY DIFFRACTION100
4.52-5.170.2431360.21772697X-RAY DIFFRACTION100
5.17-6.50.29631450.25292733X-RAY DIFFRACTION100
6.51-33.070.24441670.19512763X-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)
13.6139-1.0321-0.26042.02541.21.23320.49280.72840.1685-0.7935-0.4257-0.2489-0.6496-0.24440.09221.09230.17480.19980.87910.15530.943535.48330.243327.9448
22.97330.2926-1.27410.3512-0.26620.5401-0.05030.49551.04410.40530.19440.5122-0.9299-0.20270.24471.0094-0.0638-0.08151.12780.00480.943439.270614.54332.7181
35.77192.495-0.93671.2375-0.09070.77491.30942.4986-0.2989-0.07120.04240.0227-0.17070.52760.62371.5742-0.6175-0.15872.42410.66151.06262.543818.56322.1231
43.08050.72110.38612.6507-0.12321.5477-0.33020.3760.4748-0.04040.08550.2373-0.22540.09890.26940.7409-0.07590.09210.86170.11360.896864.681813.756523.7014
53.1026-1.17390.67022.3433-0.31421.3119-0.09330.38360.29290.1192-0.1065-0.22580.62440.22880.15760.83620.0330.27490.8148-0.05820.856359.2407-7.33123.4986
62.55311.46380.22471.9550.08532.0535-0.30920.10220.56360.11010.0449-0.5293-0.1202-0.03140.21860.5242-0.01780.21170.65670.11220.676565.021913.309728.5159
74.87672.3147-1.2671.9672-0.8051.5241-0.1868-0.2666-0.3276-0.2322-0.4432-0.8060.29320.45260.23890.7748-0.06840.19640.79980.00150.810673.490611.683634.9382
80.07970.05750.01930.1248-0.08070.1014-1.07910.6939-0.0586-0.9471-0.5417-0.1726-0.3058-1.14860.25541.6103-0.39070.40411.0521-0.2921.780125.7526-42.615832.972
92.8909-1.106-0.68292.0756-1.59772.0955-0.15520.1279-0.8166-0.42390.2128-0.38381.3339-0.49950.57511.3292-0.11750.23810.81490.08482.034930.1538-35.276336.098
100.6826-1.6601-0.15974.04590.38340.0226-0.92272.9608-2.64030.7237-0.17461.43030.40880.83190.58741.83410.10380.47191.909-0.07073.249133.1614-43.57646.3176
113.0165-2.1743-0.36362.75271.05053.3665-0.5301-0.4194-1.01650.19230.215-0.68740.89190.23820.36370.993-0.0190.32610.92330.14991.337132.956-24.880542.6021
122.49160.553-1.87493.65330.43731.49680.3738-0.3557-0.24430.0594-0.1604-0.0514-0.0686-0.1504-0.01660.9222-0.03730.02930.9501-0.03330.977926.8091-12.042136.5186
132.5689-1.2688-0.93470.89210.01055.6823-0.4026-0.6884-1.80330.45940.036-0.11990.8845-1.54410.21441.6037-0.07860.34581.44550.04652.412528.1754-37.658343.1777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 157 )
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 318 )
5X-RAY DIFFRACTION5chain 'A' and (resid 319 through 431 )
6X-RAY DIFFRACTION6chain 'A' and (resid 432 through 560 )
7X-RAY DIFFRACTION7chain 'A' and (resid 561 through 610 )
8X-RAY DIFFRACTION8chain 'E' and (resid 333 through 342 )
9X-RAY DIFFRACTION9chain 'E' and (resid 343 through 379 )
10X-RAY DIFFRACTION10chain 'E' and (resid 380 through 394 )
11X-RAY DIFFRACTION11chain 'E' and (resid 395 through 437 )
12X-RAY DIFFRACTION12chain 'E' and (resid 438 through 506 )
13X-RAY DIFFRACTION13chain 'E' and (resid 507 through 526 )

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