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- PDB-7ekh: Structure of SARS-CoV-2 spike receptor-binding domain Y453F mutat... -

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Basic information

Entry
Database: PDB / ID: 7ekh
TitleStructure of SARS-CoV-2 spike receptor-binding domain Y453F mutation complexed with human ACE2
Components
  • Angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsHYDROLASE/VIRAL PROTEIN / SARS-CoV-2 / spike / RBD / Y453F / ACE2 / VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / regulation of transmembrane transporter activity / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / Potential therapeutics for SARS / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / 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 / membrane raft / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / 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 / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane
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. / Neutral zinc metallopeptidases, zinc-binding region signature. / 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 ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / 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
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHan, P.C. / Su, C. / Zhang, Y.F. / Qi, J.X. / Gao, G.F.
CitationJournal: Nat Commun / Year: 2021
Title: Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.
Authors: Han, P. / Su, C. / Zhang, Y. / Bai, C. / Zheng, A. / Qiao, C. / Wang, Q. / Niu, S. / Chen, Q. / Zhang, Y. / Li, W. / Liao, H. / Li, J. / Zhang, Z. / Cho, H. / Yang, M. / Rong, X. / Hu, Y. / ...Authors: Han, P. / Su, C. / Zhang, Y. / Bai, C. / Zheng, A. / Qiao, C. / Wang, Q. / Niu, S. / Chen, Q. / Zhang, Y. / Li, W. / Liao, H. / Li, J. / Zhang, Z. / Cho, H. / Yang, M. / Rong, X. / Hu, Y. / Huang, N. / Yan, J. / Wang, Q. / Zhao, X. / Gao, G.F. / Qi, J.
History
DepositionApr 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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: Angiotensin-converting enzyme 2
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8687
Polymers95,9182
Non-polymers9505
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-25 kcal/mol
Surface area35000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.639, 103.639, 227.133
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Angiotensin-converting enzyme 2 / ACE-related carboxypeptidase / Angiotensin-converting enzyme homolog / ACEH / Metalloprotease MPROT15


Mass: 69982.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#2: Protein Spike protein S1


Mass: 25935.219 Da / Num. of mol.: 1 / Mutation: Y453F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#3: 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 / 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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
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: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, pH 6.5, 10% w/v PEG 5000 MME, 12% v/v1-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 49236 / % possible obs: 99.8 % / Redundancy: 18.7 % / Biso Wilson estimate: 37.12 Å2 / CC1/2: 0.998 / Net I/σ(I): 19.826
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 46716 / CC1/2: 0.565

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX1.19_4092refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6lzg

6lzg


Resolution: 2.4→20.39 Å / SU ML: 0.2312 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2608
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228 2279 4.88 %
Rwork0.2098 44437 -
obs0.2107 46716 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 57 250 6711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00496648
X-RAY DIFFRACTIONf_angle_d0.74249038
X-RAY DIFFRACTIONf_chiral_restr0.0499957
X-RAY DIFFRACTIONf_plane_restr0.00481169
X-RAY DIFFRACTIONf_dihedral_angle_d13.93692406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.450.325800.26611693X-RAY DIFFRACTION59.46
2.45-2.510.26561020.28552062X-RAY DIFFRACTION71.92
2.51-2.570.30561420.27052619X-RAY DIFFRACTION90.32
2.57-2.640.31881340.25612817X-RAY DIFFRACTION98.11
2.64-2.720.28671270.25212888X-RAY DIFFRACTION99.8
2.72-2.810.28461580.24262889X-RAY DIFFRACTION100
2.81-2.910.20791440.2362860X-RAY DIFFRACTION100
2.91-3.020.27021380.23092904X-RAY DIFFRACTION100
3.02-3.160.24211500.23412918X-RAY DIFFRACTION100
3.16-3.330.23251640.23012884X-RAY DIFFRACTION100
3.33-3.530.22671630.22532903X-RAY DIFFRACTION100
3.53-3.80.25731500.19922917X-RAY DIFFRACTION100
3.8-4.180.16551430.17972953X-RAY DIFFRACTION100
4.18-4.780.19991660.16492956X-RAY DIFFRACTION100
4.78-60.21321520.19013011X-RAY DIFFRACTION100
6-20.390.20211660.19113163X-RAY DIFFRACTION99.88
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)
10.534050738541-0.177644389622-0.2271922199180.6833844562410.1285978222931.16618643311-0.0152175421927-0.0315931786695-0.004405981720970.03844609481930.04288952906610.06810427166070.01400586466460.0595759826871-0.0288445427770.173140799333-0.02228780838160.01782794400230.251703623149-0.02657116121180.251959587904-24.430494825815.6345778789-24.6552411888
21.53849327193-0.0471130467717-0.6044979694761.510674637070.08445464046791.7041739383-0.0192654018223-0.379291622092-0.007892998426180.2685892775640.0898548431503-0.202779855949-0.03824435131830.432895741182-0.07850592256760.3133244309370.04588179534480.02973131031990.476005435081-0.02557621602990.341406486331-31.597870771525.733907195921.5200864578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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