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

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Basic information

Entry
Database: PDB / ID: 9jrc
TitleCrystal structure of SARS-CoV-2 receptor-binding domain complexed with squirrel ACE2
Components
  • Angiotensin-converting enzyme
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / 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 / 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 / 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, 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, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesPetaurus norfolcensis (squirrel glider)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 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 protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1359
Polymers91,1742
Non-polymers1,9617
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-12 kcal/mol
Surface area35030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.135, 194.135, 148.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 2 types, 2 molecules BE

#1: Protein Angiotensin-converting enzyme


Mass: 69131.984 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 protein S1


Mass: 22041.668 Da / Num. of mol.: 1
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

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Sugars , 3 types, 6 molecules

#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.: 1 / 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
#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: 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
#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

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 3.75 Å3/Da / Density % sol: 67.24 %
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: BL19U1 / 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: 3.16→50 Å / Num. obs: 24223 / % possible obs: 98.79 % / Redundancy: 25 % / CC1/2: 0.992 / Net I/σ(I): 9.5
Reflection shellResolution: 3.16→3.27 Å / Num. unique obs: 2284 / CC1/2: 0.772

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 3.16→29.65 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1263 5.22 %
Rwork0.1968 --
obs0.1985 24216 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.16→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6512 0 32 0 6544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116721
X-RAY DIFFRACTIONf_angle_d1.2899122
X-RAY DIFFRACTIONf_dihedral_angle_d5.706921
X-RAY DIFFRACTIONf_chiral_restr0.068977
X-RAY DIFFRACTIONf_plane_restr0.0111168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.290.36851210.31712417X-RAY DIFFRACTION95
3.29-3.440.33291400.27752529X-RAY DIFFRACTION99
3.44-3.620.27111500.24792521X-RAY DIFFRACTION100
3.62-3.840.23831380.21152544X-RAY DIFFRACTION100
3.84-4.140.20871490.1852553X-RAY DIFFRACTION100
4.14-4.550.20791290.17282556X-RAY DIFFRACTION100
4.55-5.210.19371570.16732582X-RAY DIFFRACTION100
5.21-6.550.22881450.20582605X-RAY DIFFRACTION100
6.55-29.650.20011340.16492646X-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)
10.06930.1077-0.06540.31490.09880.23960.1504-0.2782-0.3635-0.23950.0047-0.5585-0.44850.74150.03560.70050.0146-0.02090.77570.09650.55551.663-61.834-5.036
20.15-0.23920.15651.06980.39950.1864-0.0637-0.1927-0.3709-0.1482-0.08690.64990.05050.14960.00070.7882-0.0988-0.01970.68930.12090.8932-10.655-59.481-10.008
31.0557-0.19720.42040.89910.53730.56350.1160.163-0.0994-0.9265-0.42890.29730.1522-0.24920.00041.09550.1404-0.23570.7431-0.00620.9129-23.973-39.631-27.159
40.5785-0.60270.44881.2360.02530.5203-0.0376-0.0757-0.0646-0.1636-0.13430.31-0.0258-0.23870.00020.66020.0533-0.0370.58770.10710.6677-16.729-28.611-11.029
50.954-0.3963-0.16980.5009-0.25121.081-0.1642-0.15360.1764-0.1134-0.0687-0.33210.19770.2146-00.5401-0.03360.02720.54110.17740.61628.194-36.894-15.84
60.9856-1.35670.48081.5925-0.1830.98550.0113-0.07550.0292-0.0396-0.1780.31280.0403-0.07460.00020.5975-0.0049-0.0590.59180.09540.5439-14.1-31.964-9.839
70.529-0.3058-0.16330.95590.54390.1742-0.06330.00790.32820.1194-0.3081-0.2755-0.19650.1137-0.00050.55890.0538-0.01260.60440.10390.7-11.225-24.686-2.92
80.29390.1091-0.8140.0451-0.27412.2007-0.0230.7165-0.1773-0.9604-0.0906-0.64990.92450.0412-0.39130.70830.28610.10250.74240.28941.39435.505-73.033-4.885
90.09320.0547-0.05390.0234-0.0260.02780.0422-0.34630.324-0.2355-0.39120.1916-0.31771.5294-0.00051.1284-0.0297-0.10851.50230.3891.351240.629-60.4030.68
100.40890.19380.09670.8147-0.60710.57890.1557-0.02590.1353-0.0439-0.3142-0.218-0.01250.1566-0.00020.71150.09260.00580.73910.16620.747421.838-66.079-0.568
110.11920.1898-0.1530.3463-0.11220.40880.07360.1147-0.84930.10170.04160.0676-0.06020.2175-0.00090.74590.0442-0.0480.62280.1610.76647.838-76.5054.161
120.1091-0.0367-0.28950.35890.09860.67990.27-0.7063-0.1988-0.5052-0.2743-0.1916-0.13460.22640.01350.6721-0.0197-0.01950.74090.17240.948422.807-62.539-6.526
130.0267-0.00350.01090.00220.00750.02750.35790.41670.15410.00290.0676-0.18720.40260.1189-0.00091.2670.2509-0.01292.0440.44491.615245.97-73.469.61
141.99961.99912.00021.99982.000522.76973.2924-0.2982-2.3208-2.73890.04913.22824.1615-0.05441.315-0.079-0.0532.02520.43941.009254.514-65.7042.799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 18:51 )B18 - 51
2X-RAY DIFFRACTION2( CHAIN B AND RESID 52:129 )B52 - 129
3X-RAY DIFFRACTION3( CHAIN B AND RESID 130:193 )B130 - 193
4X-RAY DIFFRACTION4( CHAIN B AND RESID 194:293 )B194 - 293
5X-RAY DIFFRACTION5( CHAIN B AND RESID 294:431 )B294 - 431
6X-RAY DIFFRACTION6( CHAIN B AND RESID 432:561 )B432 - 561
7X-RAY DIFFRACTION7( CHAIN B AND RESID 562:613 )B562 - 613
8X-RAY DIFFRACTION8( CHAIN E AND RESID 333:364 )E333 - 364
9X-RAY DIFFRACTION9( CHAIN E AND RESID 365:393 )E365 - 393
10X-RAY DIFFRACTION10( CHAIN E AND RESID 394:459 )E394 - 459
11X-RAY DIFFRACTION11( CHAIN E AND RESID 460:494 )E460 - 494
12X-RAY DIFFRACTION12( CHAIN E AND RESID 495:516 )E495 - 516
13X-RAY DIFFRACTION13( CHAIN E AND RESID 517:526 )E517 - 526
14X-RAY DIFFRACTION14( CHAIN E AND RESID 529:530 )E529 - 530

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