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- PDB-9jte: Crystal structure of SARS-CoV-2 receptor binding domain complexed... -

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Basic information

Entry
Database: PDB / ID: 9jte
TitleCrystal structure of SARS-CoV-2 receptor binding domain complexed with fox ACE2
Components
  • Angiotensin-converting enzyme
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / 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 / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / cilium / symbiont-mediated suppression of host innate immune response / apical plasma membrane / receptor ligand activity / 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 / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / proteolysis / extracellular space / metal ion binding / identical protein binding / membrane / plasma 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
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesVulpes vulpes (red fox)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.66 Å
AuthorsJun, L. / Xiaoyan, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of SARS-CoV-2 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
B: Angiotensin-converting enzyme
E: Spike protein S1
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,36212
Polymers181,6184
Non-polymers2,7458
Water00
1
A: Angiotensin-converting enzyme
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2626
Polymers90,8092
Non-polymers1,4534
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint15 kcal/mol
Surface area34070 Å2
MethodPISA
2
B: Angiotensin-converting enzyme
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1006
Polymers90,8092
Non-polymers1,2914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint13 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.976, 192.714, 194.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Angiotensin-converting enzyme


Mass: 68935.359 Da / Num. of mol.: 2
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 protein S1


Mass: 21873.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#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.: 1 / 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: 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.: 3 / Source method: obtained synthetically
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
#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.: 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
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: 3.83 Å3/Da / Density % sol: 67.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate, 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 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.66→50 Å / Num. obs: 30800 / % possible obs: 97.81 % / Redundancy: 7.1 % / CC1/2: 0.991 / Net I/σ(I): 8.63
Reflection shellResolution: 3.66→3.79 Å / Num. unique obs: 2629 / CC1/2: 0.656

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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 / Resolution: 3.66→25 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 1551 5.05 %
Rwork0.2281 --
obs0.2292 30701 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.66→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12919 0 28 0 12947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513329
X-RAY DIFFRACTIONf_angle_d0.73518115
X-RAY DIFFRACTIONf_dihedral_angle_d4.5981802
X-RAY DIFFRACTIONf_chiral_restr0.0461921
X-RAY DIFFRACTIONf_plane_restr0.0062328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.66-3.780.26851330.28582202X-RAY DIFFRACTION84
3.78-3.920.33141180.26862713X-RAY DIFFRACTION100
3.92-4.070.28431360.2512662X-RAY DIFFRACTION100
4.07-4.260.21331520.23862659X-RAY DIFFRACTION100
4.26-4.480.24171550.22452664X-RAY DIFFRACTION100
4.48-4.760.2451500.20722663X-RAY DIFFRACTION100
4.76-5.120.23291230.2262702X-RAY DIFFRACTION100
5.12-5.630.33061250.23022718X-RAY DIFFRACTION100
5.63-6.440.30831350.2562738X-RAY DIFFRACTION100
6.44-8.060.22311820.23192687X-RAY DIFFRACTION100
8.06-250.20871420.19252742X-RAY DIFFRACTION97
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)
14.4270.6318-0.86638.6755-2.78322.14110.4762-2.25220.34361.9398-0.58160.09931.7199-1.2251-1.18141.4593-0.24250.02161.5369-0.01630.9638-19.81557.946-11.05
27.3449-3.23511.09586.56274.85065.89660.1442-0.71291.1056-0.1765-0.42450.40472.35062.443-0.2051.6623-0.03640.23851.60940.2171.1072-12.32664.928-2.488
34.07151.70870.0143.21610.07346.37410.3963-0.21610.27150.2033-0.5102-0.0887-0.13150.35730.08590.7246-0.2071-0.03270.7022-0.09540.8815-17.25568.023-29.137
43.72821.3313-1.09263.3920.57395.31020.3259-0.4151-0.13510.7637-0.25250.1173-0.0626-0.1283-0.02120.8659-0.13470.0720.7733-0.07590.7071-19.59968.513-28.149
53.1774-1.2737-0.81670.6373-0.02321.1604-0.740.7811-0.6879-0.67060.38590.11080.7110.22120.1270.9848-0.2059-0.16980.9479-0.25841.091-10.509-36.064-120.5
66.5972-2.7391-0.28067.2247-6.77088.4145-0.27730.03-2.21220.49950.6767-0.18790.4938-0.35980.32371.1911-0.1444-0.34681.0233-0.04051.1516-16.681-36.209-115.823
70.06320.48170.04386.10351.0230.19330.01880.525-0.05840.6138-0.75970.391.88251.1205-0.09611.50940.1272-0.06131.8967-0.09381.5049-26.099-43.568-112.874
87.1873-1.06150.75416.8408-0.40775.32420.4747-0.2524-0.3067-0.01560.11540.16460.1586-0.1644-0.59040.93790.0502-0.33340.7588-0.16070.752-20.392-24.777-113.4
93.7345-0.66440.58998.051-0.76466.0119-0.20520.71010.8836-0.47430.23150.0212-0.3549-0.0522-0.31960.852-0.1584-0.06190.7669-0.04920.6632-18.129-16.07-120.814
101.59770.293-1.86732.2184-1.0427.2315-0.31751.20961.2194-1.451-0.59760.9774-0.9742-0.3141-0.27961.4911-0.1389-0.8051.17330.29581.1208-25.572-2.509-127.661
113.9914-1.75950.50835.3783-2.79713.3333-0.3848-0.3548-0.38730.0860.1384-0.03980.0919-0.0535-0.07710.68120.0244-0.09480.8725-0.13320.5912-17.848-20.373-117.919
121.11080.30921.53973.41480.14872.0359-0.11780.31950.3428-0.34690.0880.4049-0.07580.1431-0.04510.8244-0.2348-0.05720.96170.07940.9307-27.03559.96-55.256
131.43320.0989-0.57913.974-0.24111.08310.47390.20320.5442-0.4463-0.5550.6565-0.3423-0.0487-0.00740.9055-0.0526-0.09330.8138-0.07270.9703-33.36737.197-69.2
141.5181-0.4667-0.57662.66921.69021.08320.1054-0.0423-0.1865-0.0731-0.11960.1654-0.0221-0.0370.02360.6815-0.1973-0.07720.6860.03070.7238-32.03232.656-52.911
153.81712.40051.75727.83693.98246.61510.91950.2148-0.74040.1579-0.5415-0.33850.6621-0.2026-0.1550.725-0.0141-0.03680.7031-0.14850.8503-25.14317.561-64.019
164.05941.42772.6110.62340.63283.69050.14150.1770.3720.0621-0.11150.1273-0.2750.3973-0.23680.8091-0.0289-0.16331.0250.12150.911-10.4826.559-109.087
172.3101-0.06351.45581.56690.08426.10960.37620.23390.3694-0.3223-0.0049-0.1637-0.42860.9866-0.22870.7524-0.0279-0.02680.9042-0.10910.8535-3.97520.365-85.852
181.2486-0.5024-0.45652.50721.41922.78680.1743-0.1249-0.03840.1516-0.008-0.0586-0.0230.1703-0.16720.5948-0.0408-0.19050.75190.01350.6268-5.584.035-81.813
194.15460.26712.74436.97954.61098.36190.4575-0.30740.10330.3132-0.1682-0.26960.1906-0.2564-0.14720.62590.0201-0.06240.8294-0.0680.6712-12.65214.83-66.742
202.93290.8089-0.65962.38730.69510.5923-0.5235-0.18491.48591.0015-0.23410.493-0.4766-0.8503-0.24470.9867-0.0689-0.07711.243-0.22661.1015-26.97671.081-12.476
212.7553-1.15090.3546.2953-2.4821.6093-0.6642-2.03240.5182.3565-0.37330.41410.7085-0.57611.08631.6815-0.3214-0.06271.6481-0.05380.9558-19.08873.072-13.037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND RESID 366:383 )E366 - 383
2X-RAY DIFFRACTION2( CHAIN E AND RESID 384:394 )E384 - 394
3X-RAY DIFFRACTION3( CHAIN E AND RESID 395:479 )E395 - 479
4X-RAY DIFFRACTION4( CHAIN E AND RESID 480:526 )E480 - 526
5X-RAY DIFFRACTION5( CHAIN C AND RESID 333:349 )C333 - 349
6X-RAY DIFFRACTION6( CHAIN C AND RESID 350:378 )C350 - 378
7X-RAY DIFFRACTION7( CHAIN C AND RESID 379:394 )C379 - 394
8X-RAY DIFFRACTION8( CHAIN C AND RESID 395:442 )C395 - 442
9X-RAY DIFFRACTION9( CHAIN C AND RESID 443:469 )C443 - 469
10X-RAY DIFFRACTION10( CHAIN C AND RESID 470:479 )C470 - 479
11X-RAY DIFFRACTION11( CHAIN C AND RESID 480:526 )C480 - 526
12X-RAY DIFFRACTION12( CHAIN A AND RESID 19:129 )A19 - 129
13X-RAY DIFFRACTION13( CHAIN A AND RESID 130:249 )A130 - 249
14X-RAY DIFFRACTION14( CHAIN A AND RESID 250:574 )A250 - 574
15X-RAY DIFFRACTION15( CHAIN A AND RESID 575:610 )A575 - 610
16X-RAY DIFFRACTION16( CHAIN B AND RESID 19:129 )B19 - 129
17X-RAY DIFFRACTION17( CHAIN B AND RESID 130:251 )B130 - 251
18X-RAY DIFFRACTION18( CHAIN B AND RESID 252:573 )B252 - 573
19X-RAY DIFFRACTION19( CHAIN B AND RESID 574:609 )B574 - 609
20X-RAY DIFFRACTION20( CHAIN E AND RESID 333:349 )E333 - 349
21X-RAY DIFFRACTION21( CHAIN E AND RESID 350:365 )E350 - 365

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