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- PDB-8if2: Crystal structure of the receptor binding domain of SARS-CoV-2 Om... -

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Basic information

Entry
Database: PDB / ID: 8if2
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 Omicron BQ.1.1 variant spike protein in complex with its receptor ACE2
Components
  • Processed angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Spike protein / RBD / ACE2
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 / negative regulation of signaling receptor activity / carboxypeptidase activity / regulation of cytokine production / positive regulation of cardiac muscle contraction / viral life cycle / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / brush border membrane / 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 / 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 / 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: 2.78 Å
AuthorsKimura, K. / Suzuki, T. / Hashiguchi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR20H8 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.
Authors: Ito, J. / Suzuki, R. / Uriu, K. / Itakura, Y. / Zahradnik, J. / Kimura, K.T. / Deguchi, S. / Wang, L. / Lytras, S. / Tamura, T. / Kida, I. / Nasser, H. / Shofa, M. / Begum, M.M. / Tsuda, M. ...Authors: Ito, J. / Suzuki, R. / Uriu, K. / Itakura, Y. / Zahradnik, J. / Kimura, K.T. / Deguchi, S. / Wang, L. / Lytras, S. / Tamura, T. / Kida, I. / Nasser, H. / Shofa, M. / Begum, M.M. / Tsuda, M. / Oda, Y. / Suzuki, T. / Sasaki, J. / Sasaki-Tabata, K. / Fujita, S. / Yoshimatsu, K. / Ito, H. / Nao, N. / Asakura, H. / Nagashima, M. / Sadamasu, K. / Yoshimura, K. / Yamamoto, Y. / Nagamoto, T. / Kuramochi, J. / Schreiber, G. / Saito, A. / Matsuno, K. / Takayama, K. / Hashiguchi, T. / Tanaka, S. / Fukuhara, T. / Ikeda, T. / Sato, K.
History
DepositionFeb 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed

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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)99,5169
Polymers95,8112
Non-polymers3,7067
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.052, 120.052, 167.416
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Space group name HallP322(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: -y,-x,-z+1/3
#5: -x+y,y,-z+2/3
#6: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11B-616-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Processed angiotensin-converting enzyme 2


Mass: 70485.102 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: 25325.590 Da / Num. of mol.: 1
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

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Sugars , 4 types, 6 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: 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

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Non-polymers , 2 types, 31 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.63 Å3/Da / Density % sol: 66.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Sodium acetate, Ammonium acetate, PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→49.17 Å / Num. obs: 34681 / % possible obs: 99.7 % / Redundancy: 20.7 % / Biso Wilson estimate: 70.65 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.4
Reflection shellResolution: 2.78→2.95 Å / Num. unique obs: 10682 / CC1/2: 0.418

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Processing

Software
NameVersionClassification
BUCCANEERmodel building
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→49.17 Å / SU ML: 0.4308 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.0878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2447 1733 5 %
Rwork0.1996 32948 -
obs0.2019 34681 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.2 Å2
Refinement stepCycle: LAST / Resolution: 2.78→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6440 0 243 30 6713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00246868
X-RAY DIFFRACTIONf_angle_d0.54739339
X-RAY DIFFRACTIONf_chiral_restr0.04551036
X-RAY DIFFRACTIONf_plane_restr0.00361181
X-RAY DIFFRACTIONf_dihedral_angle_d14.74082537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.870.38741340.32722655X-RAY DIFFRACTION97.14
2.87-2.960.31241440.2752705X-RAY DIFFRACTION100
2.96-3.060.29251450.26442738X-RAY DIFFRACTION100
3.06-3.190.32281410.25392725X-RAY DIFFRACTION100
3.19-3.330.30521480.26692759X-RAY DIFFRACTION100
3.33-3.510.28711430.24242720X-RAY DIFFRACTION100
3.51-3.730.26691480.19752734X-RAY DIFFRACTION100
3.73-4.020.23561460.19582767X-RAY DIFFRACTION99.97
4.02-4.420.22281430.17332751X-RAY DIFFRACTION100
4.42-5.060.20371430.16712773X-RAY DIFFRACTION100
5.06-6.370.23171440.18612778X-RAY DIFFRACTION100
6.37-49.170.2071540.16822843X-RAY DIFFRACTION99.67
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)
13.21733969245-1.31754088475-1.877232966341.688462954320.9663922373178.767839364230.154315747218-0.122058264118-0.1249289073780.15794413128-0.214896875031-0.494513564656-0.2485701392131.255995150420.1225188931570.457931698947-0.169250967317-0.04822634592470.6141530598560.1035453522420.60195297885640.2177586712.7861738623220.6844480405
21.36568295725-0.9471696889231.761816530511.373917361430.2236118586285.01227579540.2492775681870.3386630154480.123105344968-0.0405840926973-0.300049594244-0.99128556602-0.2319024597351.50755255660.1129371532660.651272443432-0.2350996994890.02270597890720.8997777918460.07617429805581.003165797347.08335352669.7147837435723.7492799167
34.50311946342-1.76770408056-1.508501622042.786389741052.338749306584.999425829080.063810890053-0.8866112258630.1089202669010.815988621239-0.0657566526826-0.171331082467-0.181757329360.2838807738350.03740390065761.10097187749-0.407096363289-0.2459040505530.7724829877420.08683547941870.66097869586937.881955237416.238736866551.429608735
41.93633556419-0.2583930977360.04205396882461.809939593810.3704337077472.693378455270.111296412731-0.3209291139810.5187623806150.387605895589-0.124341446786-0.439188950555-0.8462946717720.35126147263-0.01096275439550.966381309164-0.350399879161-0.08288224545990.532079193880.01783528303320.67950471386231.999779403427.17255676637.0024728264
52.47075463456-0.691745363645-0.05640289625222.143147077111.090167927681.353652276730.0726840791149-0.01083066767150.9061593430870.105459759726-0.131862663133-0.544048129585-1.047125589470.1332202271670.03895584064781.26854788257-0.2804748931030.007529433150860.5428300921170.1236404040180.86166722830531.965896057537.652573710528.5744824177
61.17809561048-1.1114316699-1.44548140913.764301940151.738380747341.80708120272-0.283649785553-0.06935188573690.0781617111179-0.384195501971-0.2249497970460.9598788075250.594886680557-0.4400123978110.4211945343070.834864597089-0.262095967213-0.03822789297360.5009036506520.06644639052740.6328588865147.19663553449-18.13755867792.5702016717
78.24908219761.871923702250.320027135822.850577999630.06428997759872.182107141490.247045335018-0.0558101990223-0.6104114234190.0863776934687-0.1938473613830.1231292196980.450202009673-0.2143889282060.02241475619750.626647240136-0.134784479275-0.02844009638280.515095839120.03721852416190.539830161398.9961911186-9.2633335762.64247177494
84.39915490282-1.959311016462.409662440242.61104163003-1.746528187315.437781412550.1340644677720.487838496769-0.115432924342-0.174666306935-0.130763441744-0.01610336665080.233792001330.0261011151343-0.01391031948050.441639112846-0.1181818380490.03566651778020.389431995584-0.02840541973360.39815408981214.2215813693-2.06653222561-0.541175495022
93.77001371018-0.5993947734880.3144660718915.231325179371.354448632295.836687741110.2729022688130.267464292674-0.4719747291120.0508155913808-0.110397964994-0.8292366958050.4950960554320.877671854632-0.2671910051540.377525071182-0.0210700258913-0.03354727658570.6844739379720.1680056581220.60248096275930.4932502333-5.900025648848.61148199133
105.67313048689-0.1810721262292.313210979674.37783162661-0.4515155973883.24073610620.1729737061210.652856881413-0.407005445125-0.192116951142-0.0627298768421-0.4340274788080.2894715130460.853421250337-0.0510262213830.4558489443310.08563894536380.05276942780150.890263959431-0.1084277858980.51096362444435.9863383788-6.59787875525-4.21863661822
114.860097383561.022896968840.3830695930312.244356881660.0210481558923.256150392510.5042849284750.21122375767-0.611904138662-0.0686467064275-0.305137069962-0.277215521160.2799778694610.33691762357-0.1410034053940.5257014536250.00142293799454-0.03596223166030.386846309710.005617276728860.34850331834822.922615024-5.840549940553.60391409349
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 82 )AA19 - 821 - 64
22chain 'A' and (resid 83 through 129 )AA83 - 12965 - 111
33chain 'A' and (resid 130 through 194 )AA130 - 194112 - 176
44chain 'A' and (resid 195 through 512 )AA195 - 512177 - 494
55chain 'A' and (resid 513 through 613 )AA513 - 613495 - 595
66chain 'B' and (resid 329 through 349 )BC329 - 3491 - 21
77chain 'B' and (resid 350 through 375 )BC350 - 37522 - 47
88chain 'B' and (resid 376 through 442 )BC376 - 44248 - 114
99chain 'B' and (resid 443 through 459 )BC443 - 459115 - 131
1010chain 'B' and (resid 460 through 479 )BC460 - 479132 - 151
1111chain 'B' and (resid 480 through 527 )BC480 - 527152 - 199

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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