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- PDB-7xby: The crystal structure of SARS-CoV-2 Omicron BA.1 variant RBD in c... -

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Basic information

Entry
Database: PDB / ID: 7xby
TitleThe crystal structure of SARS-CoV-2 Omicron BA.1 variant RBD in complex with equine ACE2
Components
  • Angiotensin-converting enzyme
  • Spike protein S1
KeywordsVIRAL PROTEIN / complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / metallopeptidase activity / 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 / 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 / apical plasma membrane / fusion of virus membrane with host plasma membrane / 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 / proteolysis / extracellular space / membrane / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / 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 ...Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / 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
BROMIDE ION / Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesEquus caballus (horse)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsXu, Z.P. / Liu, K.F. / Han, P. / Qi, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100752 China
CitationJournal: Nat Commun / Year: 2022
Title: Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses.
Authors: Xu, Z. / Kang, X. / Han, P. / Du, P. / Li, L. / Zheng, A. / Deng, C. / Qi, J. / Zhao, X. / Wang, Q. / Liu, K. / Gao, G.F.
History
DepositionMar 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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: Angiotensin-converting enzyme
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,48110
Polymers117,7152
Non-polymers7668
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-39 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.975, 113.975, 152.738
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Angiotensin-converting enzyme /


Mass: 92299.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: ACE2 / Production host: Escherichia coli (E. coli)
References: UniProt: F6V9L3, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Spike protein S1


Mass: 25415.879 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 / Variant: Omicron BA.1 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#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 / 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
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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium bromide, 0.1M Bis-Tris propane 8.5, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 27326 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 13.1
Reflection shellResolution: 2.85→2.96 Å / Rmerge(I) obs: 1.252 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2682

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Processing

Software
NameVersionClassification
PHENIX1.19rc3_4028refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 2.85→32.9 Å / SU ML: 0.3713 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.9189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2626 1252 4.89 %
Rwork0.2282 24364 -
obs0.2298 25616 93.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.83 Å2
Refinement stepCycle: LAST / Resolution: 2.85→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6416 0 21 0 6437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256613
X-RAY DIFFRACTIONf_angle_d0.58078985
X-RAY DIFFRACTIONf_chiral_restr0.041940
X-RAY DIFFRACTIONf_plane_restr0.00391162
X-RAY DIFFRACTIONf_dihedral_angle_d16.33622407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.960.3592940.33971410X-RAY DIFFRACTION50.49
2.96-3.10.3171440.29952636X-RAY DIFFRACTION92.79
3.1-3.260.31371460.28012867X-RAY DIFFRACTION99.47
3.26-3.460.3021460.28212869X-RAY DIFFRACTION99.93
3.46-3.730.26681360.24312868X-RAY DIFFRACTION99.87
3.73-4.10.25311540.21582858X-RAY DIFFRACTION99.7
4.1-4.70.26051340.19092909X-RAY DIFFRACTION99.35
4.7-5.910.22031600.19982901X-RAY DIFFRACTION99.48
5.91-32.90.22691380.20273046X-RAY DIFFRACTION99.07
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)
10.279093373193-0.3178529820570.7727997758471.31101755262-0.1481559442443.09304747128-0.04065215514050.0946062071549-0.03736060213930.00574330124109-0.0588640600365-0.395123822946-0.3825652606530.676151048747-0.05762040477230.431520439571-0.1628707838580.1134204078020.633446327634-0.01399083896170.3957802248940.6170681856-25.940554870710.3811345419
20.190502182953-0.370594141855-0.3957256289530.6484463847661.00429946841.13802852285-0.323593529672-0.00354011373013-0.4010096269320.1609606286010.3805668934-0.9543118620780.1168967410680.228782930727-0.1163669912390.43925598639-0.1578280382850.0235700820230.710339386823-0.1166770505721.0127589940946.5441227219-40.63382754197.12995341789
31.53546955628-0.05940699849670.1654419888481.622542219180.814127390791.337176467240.03628022802840.04477757450310.0575831205515-0.2329730557590.177807821995-0.472760230882-0.2628698353020.350361119943-0.08968223342440.341456196153-0.08091657305650.1330428017440.339851140873-0.1111123116310.50919580592538.5049065825-50.5264562848-12.7622471379
40.414905853958-0.127467240049-0.2663436558092.45361666561.437994752351.683836968080.007241228396390.051591467349-0.00699076838826-0.341594958361-0.0881689116471-0.00209133496306-0.272972356077-0.074970627640.06510566257020.2745684754-0.02040811751490.02245208190090.241762910063-0.01303574469980.25602291117923.4426110346-43.9739537282-9.4087340697
52.38603626198-1.66195551830.7048003982172.53148479064-0.6337753943671.4745287008-0.177454602733-0.2410347258111.4337136610.0578801014433-0.05838717174210.505774719066-0.361171392219-0.1774925400860.06808130257260.524041320893-0.102207383038-0.004802071476770.361917474474-0.1225966732780.76085620176821.66150415320.045717768055328.1190468702
62.61316516278-0.726454482888-0.4337100695072.172759932640.5537401629351.11859735302-0.0975849518862-0.322961453520.567900913541-0.446235509969-0.03214673409080.382779119351-0.443206970577-0.4334147210620.1238103195530.540749984190.0398628676414-0.01744222574270.387218346303-0.113445971270.52722383813412.2340664378-6.0147538172527.0896923847
71.688266797530.0140073135062-0.01111032965631.361031747830.2131638873561.31673862-0.0410277273336-0.2761299045650.009816662994270.191624510183-0.01860706254650.044316891440.05394840052940.1618518591340.0853158285790.396117167818-0.111166535393-0.003992239206950.3726445718610.02934762823780.24393984169427.8672804758-15.96836380629.0601843079
80.3257481161130.473206868254-0.7881251284653.28202346095-0.2161371999162.520619988260.1176479456490.319027817743-0.112021100937-0.0017232795614-0.110555702264-0.4473507904890.01196784657960.889998903250.1576233343640.386735317525-0.02751904321520.09781124523270.353657740824-0.01985633361420.22593801345536.63303877-19.293619136321.6053023649
92.30984139324-1.408662830260.5120168822493.553904926910.7507551116280.944697781543-0.0741304710434-0.7107838357270.5081272692360.686399846041-0.2670974375320.691825954485-0.348359066555-0.1830175953620.1567032878740.509849357307-0.05604658428480.07835885686440.395159664227-0.1516774540310.60669594088112.4934754406-2.7910783777834.14832007
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 250 )AA130 - 250112 - 232
44chain 'A' and (resid 251 through 614 )AA251 - 614233 - 596
55chain 'B' and (resid 333 through 358 )BC333 - 3581 - 26
66chain 'B' and (resid 359 through 409 )BC359 - 40927 - 77
77chain 'B' and (resid 410 through 479 )BC410 - 47978 - 147
88chain 'B' and (resid 480 through 506 )BC480 - 506148 - 174
99chain 'B' and (resid 507 through 527 )BC507 - 527175 - 195

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