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- PDB-7p19: Crystal structure of SARS-CoV-2 RBD Q498Y complexed with human ACE2 -

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Basic information

Entry
Database: PDB / ID: 7p19
TitleCrystal structure of SARS-CoV-2 RBD Q498Y complexed with human ACE2
Components
  • Processed angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsVIRAL PROTEIN / Viral spike / angiotensin converting enzyme-II / SARS-COV-2 / ACE-2
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 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / angiotensin maturation / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / Attachment and Entry / carboxypeptidase activity / negative regulation of signaling receptor activity / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / regulation of transmembrane transporter activity / brush border membrane / negative regulation of smooth muscle cell proliferation / cilium / negative regulation of ERK1 and ERK2 cascade / endocytic vesicle membrane / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / endopeptidase activity / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / Potential therapeutics for SARS / 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 / symbiont entry into host cell / membrane raft / apical plasma membrane / fusion of virus membrane with host plasma membrane / endoplasmic reticulum lumen / 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 / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / 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 / 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
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: 3.24 Å
AuthorsErausquin, E. / Lopez-Sagaseta, J.
Funding support Spain, 2items
OrganizationGrant numberCountry
Other government0011-3597-2020-000010 Spain
Other government0011-1408-2021-000023 Spain
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution.
Authors: Erausquin, E. / Glaser, F. / Fernandez-Recio, J. / Lopez-Sagaseta, J.
#1: Journal: Biorxiv / Year: 2021
Title: A single de novo substitution in SARS-CoV-2 spike informs enhanced adherence to human ACE2
Authors: Erausquin, E. / Lopez-Sagaseta, J.
History
DepositionJul 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Revision 1.2Jan 31, 2024Group: 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: Processed angiotensin-converting enzyme 2
E: Spike protein S1
B: Processed angiotensin-converting enzyme 2
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,59616
Polymers185,7574
Non-polymers1,83912
Water0
1
A: Processed angiotensin-converting enzyme 2
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7058
Polymers92,8782
Non-polymers8276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Processed angiotensin-converting enzyme 2
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8918
Polymers92,8782
Non-polymers1,0126
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.591, 165.037, 228.678
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 19 through 73 or resid 75...
d_2ens_1(chain "B" and (resid 19 through 20 or (resid 21...
d_1ens_2(chain "C" and (resid 339 through 360 or resid 366...
d_2ens_2(chain "E" and (resid 339 through 515 or resid 601))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERLEUA1 - 55
d_12ens_1GLUGLNA57 - 84
d_13ens_1SERGLUA88 - 209
d_14ens_1THRALAA211 - 596
d_15ens_1NAGNAGB
d_16ens_1ZNZNC
d_17ens_1NAGNAGD
d_18ens_1EDOEDOE
d_21ens_1SERLEUH1 - 55
d_22ens_1GLUGLUH57 - 206
d_23ens_1THRALAH208 - 593
d_24ens_1NAGNAGI
d_25ens_1ZNZNJ
d_26ens_1NAGNAGK
d_27ens_1EDOEDOL
d_11ens_2GLYASNN3 - 24
d_12ens_2SERPHEN30 - 179
d_13ens_2NAGNAGO
d_21ens_2GLYPHEF1 - 172
d_22ens_2NAGNAGG

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.800970354604, -0.397256866793, 0.447921279726), (-0.389719059262, 0.913896491224, 0.113632117713), (-0.454494824936, -0.0835475021399, -0.886822569059)1.42537603178, 29.9714625758, -129.881355866
2given(-0.812239725206, -0.387851668958, -0.43570369712), (-0.399721816836, 0.914071927805, -0.0685199236981), (0.424840085141, 0.118505669419, -0.897478305238)-45.0455752146, -36.0173286683, -121.255185746

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Components

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Protein , 2 types, 4 molecules ABEC

#1: Protein Processed angiotensin-converting enzyme 2


Mass: 69307.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Remaining N-terminal GP motif from 3C site / Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BYF1
#2: Protein Spike protein S1


Mass: 23570.553 Da / Num. of mol.: 2 / Mutation: Q498Y
Source method: isolated from a genetically manipulated source
Details: Remaining N-terminal GP motif from 3C site
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2

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Sugars , 1 types, 7 molecules

#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / 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 , 3 types, 5 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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Details

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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium phosphate pH 6.5, 12% w/v PEG 8000 / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2021
RadiationMonochromator: Si(111) channel-out / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.236→133.825 Å / Num. obs: 37398 / % possible obs: 99.43 % / Redundancy: 5.4 % / Biso Wilson estimate: 85.19 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.121 / Rrim(I) all: 0.284 / Net I/σ(I): 7.4
Reflection shellResolution: 3.236→3.292 Å / Rmerge(I) obs: 1.848 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1827 / CC1/2: 0.592 / Rpim(I) all: 0.838 / Rrim(I) all: 2.033 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 3.24→93.99 Å / SU ML: 0.4803 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.3763
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2885 1853 4.95 %
Rwork0.2309 35545 -
obs0.2338 37398 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.73 Å2
Refinement stepCycle: LAST / Resolution: 3.24→93.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12482 0 109 0 12591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001812962
X-RAY DIFFRACTIONf_angle_d0.492617616
X-RAY DIFFRACTIONf_chiral_restr0.03831860
X-RAY DIFFRACTIONf_plane_restr0.00392270
X-RAY DIFFRACTIONf_dihedral_angle_d4.78871731
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.774805217601
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.02052739949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.320.39551460.36322698X-RAY DIFFRACTION99.75
3.32-3.420.41461330.33252689X-RAY DIFFRACTION99.86
3.42-3.530.33641210.28892733X-RAY DIFFRACTION99.72
3.53-3.660.37831380.26752701X-RAY DIFFRACTION99.75
3.66-3.80.26111440.25332709X-RAY DIFFRACTION99.58
3.8-3.980.30331650.23412657X-RAY DIFFRACTION99.47
3.98-4.190.32291420.22942720X-RAY DIFFRACTION99.79
4.19-4.450.29821450.21382712X-RAY DIFFRACTION99.48
4.45-4.790.24631320.19772730X-RAY DIFFRACTION99.27
4.79-5.280.24261410.19892723X-RAY DIFFRACTION99.31
5.28-6.040.30691580.21862765X-RAY DIFFRACTION99.32
6.04-7.610.26211350.22072818X-RAY DIFFRACTION99.39
7.61-93.990.24691530.20952890X-RAY DIFFRACTION98.13
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)
10.73998427718-0.1546281716650.4121371136361.301341071780.6642402667052.533790988-0.0550263698423-0.03093220898580.03111533663450.00288483384040.1354300026480.0205239529654-0.250172252670.0131086166401-0.07379608430830.639143840162-0.024778012510.04081004326660.4757117986450.04114627146620.482976791378-4.6203317870744.985853944-33.7439469691
21.41910917491-0.3227500374980.3387589449573.42665004707-0.406259974972.566409714020.1423568447590.0380057882225-0.0226165670226-0.159154366340.09175878772520.1488863449360.5684603209790.263063945977-0.2273906119380.9468293418320.0801249397732-0.02162388840520.622120887208-0.03144673330860.5208014306940.7659492528454.81016760596-56.9248693523
30.732872156358-0.393309107350.4195579807752.9760195167-1.288732618042.405772090670.158613342905-0.0674476488633-0.121569082498-0.377194139233-0.02918299117270.2713877113480.10230741422-0.190904280081-0.1295635170080.8609559274350.0706416903334-0.04130815064990.6987015404420.06640900900090.618148292705-27.851971974368.855667457-101.495819265
42.244223730220.4245172834340.1711155341052.210531266270.2150689117762.383342203760.3418575808610.323208278539-0.3584141290390.04918429228960.2479887062650.330776731290.759968412013-0.278168521747-0.5655487631921.28048555501-0.0390393540951-0.3153680837640.8352750447150.1705416659221.02400480775-26.727335713826.431385468-80.6694807199
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11(chain A and resseq 19:704)AA - E19 - 704
22(chain E and resseq 339:601)EF - G339 - 601
33(chain B and resseq 19:705)BH - M19 - 705
44(chain C and resseq 337:601)CN - O337 - 601

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