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- PDB-7w6u: Structure of SARS-CoV-2 spike receptor-binding domain complexed w... -

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Basic information

Entry
Database: PDB / ID: 7w6u
TitleStructure of SARS-CoV-2 spike receptor-binding domain complexed with its receptor equine ACE2
Components
  • Angiotensin-converting enzyme
  • Spike protein S1
KeywordsVIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / proteolysis / extracellular space / membrane / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus ...Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesEquus caballus (horse)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsXu, Z.P. / Liu, K.F. / Han, P. / Qi, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100752 China
CitationJournal: Nat Commun / Year: 2022
Title: Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses
Authors: Xu, Z. / Kang, X. / Han, P. / Du, P. / Li, L. / Zheng, A. / Deng, C. / Qi, J. / Zhao, X. / Wang, Q. / Liu, K. / Gao, G.F.
History
DepositionDec 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Source and taxonomy / Structure summary / Category: entity / entity_name_com / entity_src_gen
Item: _entity.pdbx_ec / _entity.pdbx_fragment ..._entity.pdbx_ec / _entity.pdbx_fragment / _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 1.2Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0154
Polymers95,7292
Non-polymers2872
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, crystal structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-39 kcal/mol
Surface area33630 Å2
Unit cell
Length a, b, c (Å)195.570, 195.570, 149.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#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,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#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 Angiotensin-converting enzyme /


Mass: 69777.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: ACE2 / Production host: Escherichia coli (E. coli)
References: UniProt: F6V9L3, angiotensin-converting enzyme 2
#2: Protein Spike protein S1


Mass: 25951.219 Da / Num. of mol.: 1 / Fragment: UNP residues 319-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.74 Å3/Da / Density % sol: 67.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 10% (w/v) PEG 1000, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.56→31.39 Å / Num. obs: 46770 / % possible obs: 99.9 % / Redundancy: 26.8 % / Biso Wilson estimate: 58.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.034 / Rrim(I) all: 0.175 / Net I/σ(I): 17.8
Reflection shellResolution: 2.56→2.63 Å / Redundancy: 26.6 % / Num. unique obs: 3434 / CC1/2: 0.728 / Rpim(I) all: 0.45 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19rc3_4028refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 2.56→19.21 Å / SU ML: 0.3213 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.543
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2265 2363 5.07 %
Rwork0.1934 44277 -
obs0.195 46640 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.7 Å2
Refinement stepCycle: LAST / Resolution: 2.56→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 0 15 71 6440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416546
X-RAY DIFFRACTIONf_angle_d0.73228889
X-RAY DIFFRACTIONf_chiral_restr0.0452928
X-RAY DIFFRACTIONf_plane_restr0.00551150
X-RAY DIFFRACTIONf_dihedral_angle_d17.34632378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.610.33311440.30322591X-RAY DIFFRACTION99.96
2.61-2.670.37211480.28972558X-RAY DIFFRACTION100
2.67-2.730.34931330.29452549X-RAY DIFFRACTION100
2.73-2.80.28351220.27032592X-RAY DIFFRACTION100
2.8-2.870.31691390.2562587X-RAY DIFFRACTION100
2.87-2.960.27211250.25012588X-RAY DIFFRACTION100
2.96-3.050.27381510.25382567X-RAY DIFFRACTION100
3.05-3.160.29171380.24352574X-RAY DIFFRACTION99.89
3.16-3.290.29581570.23832574X-RAY DIFFRACTION100
3.29-3.440.25441190.23092601X-RAY DIFFRACTION99.96
3.44-3.620.23521470.21012601X-RAY DIFFRACTION100
3.62-3.840.25231450.18862607X-RAY DIFFRACTION99.96
3.84-4.140.18951450.16492594X-RAY DIFFRACTION99.93
4.14-4.550.16721520.15132611X-RAY DIFFRACTION100
4.55-5.190.17531420.15592626X-RAY DIFFRACTION100
5.19-6.50.22191300.17962678X-RAY DIFFRACTION100
6.5-19.210.17041260.14822779X-RAY DIFFRACTION99.76

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