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- PDB-8asy: SARS-CoV-2 Omicron BA.2.75 RBD in complex with ACE2 -

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Basic information

Entry
Database: PDB / ID: 8asy
TitleSARS-CoV-2 Omicron BA.2.75 RBD in complex with ACE2
Components
  • Processed angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS CoV-2 / Omicron / BA.2.75 / ACE2 / complex / spike / RBD
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
TRIETHYLENE GLYCOL / Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsZhou, D. / Huo, J. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Cell Rep / Year: 2022
Title: A delicate balance between antibody evasion and ACE2 affinity for Omicron BA.2.75.
Authors: Huo, J. / Dijokaite-Guraliuc, A. / Liu, C. / Zhou, D. / Ginn, H.M. / Das, R. / Supasa, P. / Selvaraj, M. / Nutalai, R. / Tuekprakhon, A. / Duyvesteyn, H.M.E. / Mentzer, A.J. / Skelly, D. / ...Authors: Huo, J. / Dijokaite-Guraliuc, A. / Liu, C. / Zhou, D. / Ginn, H.M. / Das, R. / Supasa, P. / Selvaraj, M. / Nutalai, R. / Tuekprakhon, A. / Duyvesteyn, H.M.E. / Mentzer, A.J. / Skelly, D. / Ritter, T.G. / Amini, A. / Bibi, S. / Adele, S. / Johnson, S.A. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Plowright, M. / Newman, T.A.H. / Hornsby, H. / de Silva, T.I. / Temperton, N. / Klenerman, P. / Barnes, E. / Dunachie, S.J. / Pollard, A.J. / Lambe, T. / Goulder, P. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
History
DepositionAug 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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: Processed angiotensin-converting enzyme 2
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,91222
Polymers95,2942
Non-polymers2,61820
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint5 kcal/mol
Surface area35600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.261, 105.261, 220.753
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

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Protein , 2 types, 2 molecules AB

#1: Protein Processed angiotensin-converting enzyme 2


Mass: 70139.758 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: Homo sapiens (human) / References: UniProt: Q9BYF1
#2: Protein Spike protein S1


Mass: 25154.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

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Sugars , 1 types, 6 molecules

#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.: 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

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Non-polymers , 3 types, 14 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4

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Details

Has ligand of interestN
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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1% (w/v) n-Octyl-b-D-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 5.5 and 22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.85→76.2 Å / Num. obs: 29749 / % possible obs: 99.8 % / Redundancy: 26.8 % / Biso Wilson estimate: 58 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.443 / Rpim(I) all: 0.086 / Net I/σ(I): 7.6
Reflection shellResolution: 2.85→2.9 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1411 / CC1/2: 0.279 / % possible all: 96.9

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Processing

Software
NameVersionClassification
GDA1.20.1_4487data collection
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZF7

7zf7


Resolution: 2.85→76.18 Å / SU ML: 0.4938 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2647 1439 4.87 %
Rwork0.2173 28089 -
obs0.2195 29528 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.5 Å2
Refinement stepCycle: LAST / Resolution: 2.85→76.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6464 0 167 0 6631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00166802
X-RAY DIFFRACTIONf_angle_d0.43359219
X-RAY DIFFRACTIONf_chiral_restr0.0386974
X-RAY DIFFRACTIONf_plane_restr0.00331178
X-RAY DIFFRACTIONf_dihedral_angle_d11.55012463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.950.38211380.36432540X-RAY DIFFRACTION92.28
2.95-3.070.37821600.34322749X-RAY DIFFRACTION99.52
3.07-3.210.37041300.32592794X-RAY DIFFRACTION99.66
3.21-3.380.36031640.26782761X-RAY DIFFRACTION99.63
3.38-3.590.30631270.23942797X-RAY DIFFRACTION99.73
3.59-3.870.26481320.22672816X-RAY DIFFRACTION99.76
3.87-4.260.21511420.192829X-RAY DIFFRACTION99.9
4.26-4.870.21641540.17432840X-RAY DIFFRACTION100
4.87-6.140.24491430.19792896X-RAY DIFFRACTION99.87
6.14-76.180.23941490.18733067X-RAY DIFFRACTION99.84
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)
10.159473784575-0.38304072210.2386743779420.8101112267670.6509016636681.2341767955-0.1178120163020.00135579922680.08136781587770.04632460161940.00357031924460.276616798941-0.25040986252-0.15970747429-0.04731766638110.701620478461-0.008282095498570.1024130352070.930822589758-0.05054939046740.78773979125-38.353548029229.7495917875-11.3509502094
21.41922252183-1.44074005793-0.6430729389161.60773151093-0.07500736208261.779594774450.07880006051490.185988704962-0.0696376129959-0.0151974862851-0.2023428468470.03902533014470.180675846426-0.5123993319320.05715661544510.608718142097-0.0165040415706-0.08492313885970.695882966404-0.07266289687310.664507638271-38.046337588210.9271960321-37.8029456594
31.014721920920.03071943524010.089967417371.73631924052-0.2198649541121.42518171215-0.03465647601810.1163537044410.0511888357567-0.2017049603960.06822439073520.119025001127-0.04360079262160.184265951357-0.02829023259890.540933354193-0.05236211982420.02874423393720.677202602923-0.0633887430850.604769027512-17.713843113615.6473018453-33.9064226702
40.282563510742-0.0734438947114-0.04362021143790.6382572791310.2224093219050.5922808903370.032848835662-0.00126879875182-0.1920160213790.24004493619-0.1565578411950.216972268690.2773636781230.0865879197060.03124612463460.742369582118-0.02242970875410.04893057814140.870551919203-0.0408984185710.678569097811-21.09659371466.6274408585-8.90163281853
50.89220854787-0.3268092286040.06727936245740.933339024985-0.3114800389690.6204404178740.0582320651774-0.1518239914130.1482885618490.0209088528555-0.00962451470681-0.0784238149478-0.0960941945750.0802037724097-0.01505654019840.575178021593-0.04568028191970.02793465224460.70935958148-0.06671543341710.606327393687-16.312352860417.0053957825-30.1160674187
61.133163325680.2788642215950.1061965709281.057463779050.4783916646850.618235255454-0.240097221338-0.171108256535-0.6182454841510.05691554352120.4016643686580.128243996230.7259157665850.0866370325673-0.02728049080830.8747277792530.1481832598720.08689336552050.959541341614-0.04751251828130.781222928092-37.362241586623.012544186431.9431894441
70.0974643720322-0.1358944516340.04018181867140.149464749629-0.02917622675940.006969980148440.009454423176890.4321854054450.0804039284628-0.0871820449473-0.3509630035640.08186710032851.282557658570.5704363170580.03089881759961.244069776970.203476803768-0.04639702026691.23764226587-0.1693315562351.11184679696-25.692972676515.729590324329.2319362444
81.14871024095-0.5366818585880.6332195039911.26512037006-0.8298125212720.6076529099640.0991599609022-1.3840386293-0.6632994869830.551336481930.846183511751.54382066967-0.0699184360126-0.726531667227-0.01558892915921.00897673520.172904263892-0.07404159512131.00264820151-0.1483778392511.01952428759-21.179191255522.047741237139.850807635
90.734341885698-0.411142822608-0.4530454400180.48979818040.1607048872340.621739492058-0.3448591109250.0933772877751-0.219119765984-0.0510068618657-0.115301132232-0.2866426942140.3913557799580.836876946964-0.03680662696490.871882948301-0.1151468216890.02986443478420.973603485383-0.0887294892110.7796488786-28.454559244729.600185490720.1743350411
101.18129992431-0.706169740279-0.6360865169192.22042198530.4556333483911.48856694062-0.0504271216317-0.0564856893715-0.08495631197790.1849963709290.150192808447-0.129661789579-0.1425181602990.296393616901-0.07174996743810.749021067353-0.1047344424020.03850363889020.799347020411-0.08184697714870.789188797377-35.238163296331.296388559915.0806227879
110.0209984134841-0.5301818063550.4782805110295.24665252189-5.231723723755.290091926640.132247837617-0.209164951843-0.4686137139010.5733988910450.6216248340620.2210463660430.0358198247988-0.273753135839-0.03105280367481.475795928880.0765248646482-0.0583605399831.42309426357-0.07955574006540.942852505126-27.167078644225.605381081348.8857115749
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 129 )AA19 - 1291 - 111
22chain 'A' and (resid 130 through 193 )AA130 - 193112 - 175
33chain 'A' and (resid 194 through 293 )AA194 - 293176 - 275
44chain 'A' and (resid 294 through 431 )AA294 - 431276 - 413
55chain 'A' and (resid 432 through 614 )AA432 - 614414 - 596
66chain 'B' and (resid 334 through 364 )BC334 - 3641 - 31
77chain 'B' and (resid 365 through 380 )BC365 - 38032 - 47
88chain 'B' and (resid 381 through 393 )BC381 - 39348 - 60
99chain 'B' and (resid 394 through 421 )BC394 - 42161 - 88
1010chain 'B' and (resid 422 through 516 )BC422 - 51689 - 183
1111chain 'B' and (resid 517 through 533 )BC517 - 533184 - 200

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