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- PDB-7f5r: Crystal structure of SARS-CoV-2 Y453F-RBD bound to mink ACE2 -

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Basic information

Entry
Database: PDB / ID: 7f5r
TitleCrystal structure of SARS-CoV-2 Y453F-RBD bound to mink ACE2
Components
  • Spike protein S1
  • mink ACE2
KeywordsVIRAL PROTEIN/PROTEIN BINDING / SARS-CoV-2 / receptor-binding domain / Y453F variant / mink-ACE2 / VIRAL PROTEIN / VIRAL PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / 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 / membrane / identical protein binding / 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 / 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 ...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
Biological speciesNeovison vison (American mink)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsWang, X.Q. / Ding, Q. / Lan, J. / Ren, W.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of SARS-CoV-2 Y453F-RBD bound to mink ACE2
Authors: Wang, X.Q. / Ding, Q. / Lan, J. / Ren, W.L.
History
DepositionJun 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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: mink ACE2
E: Spike protein S1
B: mink ACE2
C: Spike protein S1
D: mink ACE2
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,02115
Polymers275,4786
Non-polymers2,5439
Water00
1
A: mink ACE2
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0606
Polymers91,8262
Non-polymers1,2344
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mink ACE2
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4905
Polymers91,8262
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: mink ACE2
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4724
Polymers91,8262
Non-polymers6462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)290.185, 130.185, 136.887
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein mink ACE2


Mass: 69733.227 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neovison vison (American mink) / Production host: Trichoplusia ni (cabbage looper)
#2: Protein Spike protein S1


Mass: 22092.758 Da / Num. of mol.: 3
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 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.: 2
Source method: isolated from a genetically manipulated source
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 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}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.: 6 / 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 interestN

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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: 4.72 Å3/Da / Density % sol: 73.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 1.6M sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.01→43.53 Å / Num. obs: 101471 / % possible obs: 98.12 % / Redundancy: 9.9 % / CC1/2: 0.977 / Rpim(I) all: 0.078 / Net I/σ(I): 7.71
Reflection shellResolution: 3.01→3.12 Å / Num. unique obs: 9547 / CC1/2: 0.589 / Rpim(I) all: 0.447

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6m0j

6m0j


Resolution: 3.01→43.53 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 5072 5 %
Rwork0.1812 96346 -
obs0.1831 101418 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.23 Å2 / Biso mean: 65.5468 Å2 / Biso min: 35.84 Å2
Refinement stepCycle: final / Resolution: 3.01→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19222 0 164 0 19386
Biso mean--96.22 --
Num. residues----2357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.01-3.040.33411290.2992602273180
3.04-3.080.34971660.281331893355100
3.08-3.120.35491750.27833239341499
3.12-3.160.31241620.26543213337599
3.16-3.20.26041510.255632563407100
3.2-3.240.32941700.26673186335699
3.24-3.290.30191830.26493166334999
3.29-3.340.33261830.26263255343899
3.34-3.390.29831610.243732033364100
3.39-3.450.27991880.235832243412100
3.45-3.50.24851650.21353234339999
3.5-3.570.2381850.204231963381100
3.57-3.640.26431780.20563232341099
3.64-3.710.22511580.20593231338999
3.71-3.790.24971420.17833269341199
3.79-3.880.2131730.17823202337599
3.88-3.980.20431780.16793238341699
3.98-4.080.19661790.17123209338899
4.08-4.20.21141620.16343240340299
4.2-4.340.20191650.15433216338198
4.34-4.50.17261770.14323247342499
4.5-4.670.17331610.13543230339199
4.67-4.890.18951680.1333252342099
4.89-5.140.16481810.1383216339799
5.14-5.470.17921700.14363276344699
5.47-5.890.19231800.15823243342398
5.89-6.480.20151700.16233248341898
6.48-7.410.18671750.16753266344198
7.41-9.320.16951830.14773311349498
9.32-43.530.19871540.18923257341192
Refinement TLS params.Method: refined / Origin x: 47.8286 Å / Origin y: 75.2513 Å / Origin z: 44.7871 Å
111213212223313233
T0.4127 Å20.0175 Å20.0092 Å2-0.3494 Å20.0306 Å2--0.3364 Å2
L0.7955 °20.0628 °2-0.0295 °2-0.3093 °2-0.0576 °2--0.3535 °2
S-0.0198 Å °0.0646 Å °-0.0154 Å °-0.0052 Å °-0.028 Å °-0.0394 Å °-0.0039 Å °0.079 Å °0.0445 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA19 - 902
2X-RAY DIFFRACTION1allA903 - 907
3X-RAY DIFFRACTION1allE335 - 529
4X-RAY DIFFRACTION1allB19 - 902
5X-RAY DIFFRACTION1allB903 - 905
6X-RAY DIFFRACTION1allC333 - 528
7X-RAY DIFFRACTION1allD19 - 902
8X-RAY DIFFRACTION1allD903 - 905
9X-RAY DIFFRACTION1allF332 - 528

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