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- PDB-7e3j: Crystal structure of SARS-CoV-2 RBD binding to dog ACE2 -

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Basic information

Entry
Database: PDB / ID: 7e3j
TitleCrystal structure of SARS-CoV-2 RBD binding to dog ACE2
Components
  • ACE2
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / spike / RBD / receptor binding
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / 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 / symbiont-mediated suppression of host innate immune response / 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 / identical protein binding / membrane / plasma membrane
Similarity search - Function
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 ...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
Biological speciesCanis lupus familiaris (dog)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsZhang, Z. / Zhang, Y.
CitationJournal: Nat Commun / Year: 2021
Title: The molecular basis for SARS-CoV-2 binding to dog ACE2.
Authors: Zhang, Z. / Zhang, Y. / Liu, K. / Li, Y. / Lu, Q. / Wang, Q. / Zhang, Y. / Wang, L. / Liao, H. / Zheng, A. / Ma, S. / Fan, Z. / Li, H. / Huang, W. / Bi, Y. / Zhao, X. / Wang, Q. / Gao, G.F. ...Authors: Zhang, Z. / Zhang, Y. / Liu, K. / Li, Y. / Lu, Q. / Wang, Q. / Zhang, Y. / Wang, L. / Liao, H. / Zheng, A. / Ma, S. / Fan, Z. / Li, H. / Huang, W. / Bi, Y. / Zhao, X. / Wang, Q. / Gao, G.F. / Xiao, H. / Tong, Z. / Qi, J. / Sun, Y.
History
DepositionFeb 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 28, 2021Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Aug 25, 2021Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 13, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.5Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACE2
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4164
Polymers106,1292
Non-polymers2872
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-39 kcal/mol
Surface area39070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.256, 168.256, 211.196
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein ACE2


Mass: 84255.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
#2: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 21873.496 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: Insect cell expression vector pTIE1 (others)
References: UniProt: P0DTC2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Sequence detailsThe NCBI reference sequence for dog ACE2 is XP_025292925.2.

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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: 3.63 Å3/Da / Density % sol: 66.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2% 1,4-dioxane, 0.1 M tris pH 8.0,15% polyethylene glycol 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 30355 / % possible obs: 98.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 56.13 Å2 / CC1/2: 0.98 / Net I/σ(I): 8.8
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2989 / CC1/2: 0.819

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 2.99→48.26 Å / SU ML: 0.4216 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8093
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2479 1458 4.91 %
Rwork0.2272 28210 -
obs0.2282 29668 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.64 Å2
Refinement stepCycle: LAST / Resolution: 2.99→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7244 0 1 0 7245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00247449
X-RAY DIFFRACTIONf_angle_d0.531210122
X-RAY DIFFRACTIONf_chiral_restr0.0411061
X-RAY DIFFRACTIONf_plane_restr0.00441308
X-RAY DIFFRACTIONf_dihedral_angle_d22.67592721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.10.36171240.32222551X-RAY DIFFRACTION88.69
3.1-3.220.36921470.29782689X-RAY DIFFRACTION93.26
3.22-3.370.31981330.28622790X-RAY DIFFRACTION95.84
3.37-3.550.32461620.27292836X-RAY DIFFRACTION98.88
3.55-3.770.26271530.23822872X-RAY DIFFRACTION98.73
3.77-4.060.24371380.21722850X-RAY DIFFRACTION98.1
4.06-4.470.20091590.19282839X-RAY DIFFRACTION97.59
4.47-5.120.18881360.1822901X-RAY DIFFRACTION97.87
5.12-6.450.23341480.21912912X-RAY DIFFRACTION97.95
6.45-48.260.21151580.20672970X-RAY DIFFRACTION95.45
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)
10.2994143994290.251317689835-0.1827911155160.12121010655-0.02936119002760.2172026608960.0158350996486-0.004735056759750.00897234279021-0.0311087935679-0.04205003712340.00450524654605-0.04869154911970.0530098075803-2.3723901725E-110.244188657270.02936392812180.01700668767790.287824968965-0.001180648668350.261140592489-60.539390763230.9174223266-25.6703155624
20.173540095185-0.06713567900570.01623312795710.114484187009-0.09364840710750.0637844898838-0.0492849951693-0.0227033174420.00909275607422-0.004512964946180.0667738306870.1346965674710.117101985577-0.05185462881214.63316469626E-90.2853266780710.0298500257191-0.0214213264810.330858365852-0.01304964161330.316109935019-112.6122626423.6311309937-17.8611689045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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