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- PDB-7wbp: Crystal structure of the receptor binding domain of SARS-CoV-2 Om... -

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Basic information

Entry
Database: PDB / ID: 7wbp
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with its receptor human ACE2
Components
  • Angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsVIRAL PROTEIN / Complex
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 / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy ...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 / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy / peptidyl-dipeptidase activity / regulation of vasoconstriction / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / Attachment and Entry / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / negative regulation of transcription by RNA polymerase II / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
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 Å
AuthorsQi, J. / Han, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell / Year: 2022
Title: Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2.
Authors: Pengcheng Han / Linjie Li / Sheng Liu / Qisheng Wang / Di Zhang / Zepeng Xu / Pu Han / Xiaomei Li / Qi Peng / Chao Su / Baihan Huang / Dedong Li / Rong Zhang / Mingxiong Tian / Lutang Fu / ...Authors: Pengcheng Han / Linjie Li / Sheng Liu / Qisheng Wang / Di Zhang / Zepeng Xu / Pu Han / Xiaomei Li / Qi Peng / Chao Su / Baihan Huang / Dedong Li / Rong Zhang / Mingxiong Tian / Lutang Fu / Yuanzhu Gao / Xin Zhao / Kefang Liu / Jianxun Qi / George F Gao / Peiyi Wang /
Abstract: The coronavirus disease 2019 (COVID-19) pandemic continues worldwide with many variants arising, some of which are variants of concern (VOCs). A recent VOC, omicron (B.1.1.529), which obtains a large ...The coronavirus disease 2019 (COVID-19) pandemic continues worldwide with many variants arising, some of which are variants of concern (VOCs). A recent VOC, omicron (B.1.1.529), which obtains a large number of mutations in the receptor-binding domain (RBD) of the spike protein, has risen to intense scientific and public attention. Here, we studied the binding properties between the human receptor ACE2 (hACE2) and the VOC RBDs and resolved the crystal and cryoelectron microscopy structures of the omicron RBD-hACE2 complex as well as the crystal structure of the delta RBD-hACE2 complex. We found that, unlike alpha, beta, and gamma, omicron RBD binds to hACE2 at a similar affinity to that of the prototype RBD, which might be due to compensation of multiple mutations for both immune escape and transmissibility. The complex structures of omicron RBD-hACE2 and delta RBD-hACE2 reveal the structural basis of how RBD-specific mutations bind to hACE2.
History
DepositionDec 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 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: Angiotensin-converting enzyme 2
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0509
Polymers94,4542
Non-polymers1,5967
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-18 kcal/mol
Surface area35310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.238, 104.238, 227.178
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

#1: Protein Angiotensin-converting enzyme 2 / ACE-related carboxypeptidase / Angiotensin-converting enzyme homolog


Mass: 69038.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#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 / Production host: Homo sapiens (human) / 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.: 1
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: 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.: 5 / 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
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES pH 6.5,10%w/v PEG 5000 MME,12% v/v 1-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 25810 / % possible obs: 99.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 55.69 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.07 / Rrim(I) all: 0.199 / Rsym value: 0.19 / Net I/σ(I): 10.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2509 / CC1/2: 0.692 / CC star: 0.904 / Rpim(I) all: 0.404 / Rrim(I) all: 1.142 / % possible all: 100

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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: 3→46.62 Å / SU ML: 0.3003 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1871
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2037 2831 7.85 %
Rwork0.1809 33242 -
obs0.1827 25268 75.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.9 Å2
Refinement stepCycle: LAST / Resolution: 3→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6427 0 99 0 6526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036718
X-RAY DIFFRACTIONf_angle_d0.61879134
X-RAY DIFFRACTIONf_chiral_restr0.0444975
X-RAY DIFFRACTIONf_plane_restr0.00491175
X-RAY DIFFRACTIONf_dihedral_angle_d7.5411919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.060.2881770.2678892X-RAY DIFFRACTION40.73
3.06-3.110.2502910.25921073X-RAY DIFFRACTION49.16
3.11-3.170.3173990.25391135X-RAY DIFFRACTION51.35
3.17-3.240.2641990.25451169X-RAY DIFFRACTION53.37
3.24-3.310.28621040.25321191X-RAY DIFFRACTION54.76
3.31-3.380.29171060.23381262X-RAY DIFFRACTION56.41
3.38-3.470.24231090.2181254X-RAY DIFFRACTION57.63
3.47-3.560.23461060.2031327X-RAY DIFFRACTION60.77
3.56-3.670.23321170.2011421X-RAY DIFFRACTION64.16
3.67-3.780.2431330.19161518X-RAY DIFFRACTION69.14
3.78-3.920.16661440.17141644X-RAY DIFFRACTION74.97
3.92-4.080.17281620.15711868X-RAY DIFFRACTION85.55
4.08-4.260.20921800.15992116X-RAY DIFFRACTION96.88
4.26-4.490.14931980.15552206X-RAY DIFFRACTION99.92
4.49-4.770.17181900.14992215X-RAY DIFFRACTION100
4.77-5.130.17991850.15212166X-RAY DIFFRACTION100
5.14-5.650.20591870.17212203X-RAY DIFFRACTION100
5.65-6.470.20931830.19842215X-RAY DIFFRACTION100
6.47-8.140.20331800.17872197X-RAY DIFFRACTION100
8.14-46.620.19871810.17622170X-RAY DIFFRACTION98.62
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)
11.52728123435-0.261859541691-0.7073281554594.186922140.279491474241.882033608740.1378012723770.2607972282140.2001989933950.09424542513450.01275024537320.725544644418-0.212237577657-0.518652803851-0.1632986764930.3659659265010.08066961013980.0789406558620.5768490656580.04532282194150.432888555781-39.742533715525.9604139791-7.10864643464
20.536036363379-0.1708459675840.5052763424950.0279703797616-0.1606963060191.4846552511-0.1664514317140.05539203680710.2919875665780.201366834645-0.02256644993860.255112893657-0.404593739249-0.07307145649950.1670719009110.4791772132390.04752585690090.1106990552090.421657670558-0.06264034793050.562834928474-36.99148548933.3800742422-20.2603674605
32.0229007109-1.71795860364-0.6379666298662.520926848320.1238884416962.49796130647-0.009822329617950.21784844645-0.326468938848-0.190113972882-0.1233403969240.7173768840610.231167474323-0.5541219613180.1181504939720.267597260934-0.0455881492079-0.008770718508450.436595527916-0.05636616763920.402600971324-38.656022137411.4873552429-39.4343003325
41.56906032377-0.281204909851-0.175308164511.684443525510.7126834264812.210585624-0.07838537386760.08894525721920.0352272863914-0.1384897200840.139428544519-0.0535790259418-0.0491721495450.207589656142-0.07156242578480.250018761184-0.05143992358710.01476575614840.319557175141-0.02333841618630.267386303527-18.141164805315.6459228335-35.4355974684
51.7072962697-0.396121809335-0.4928456233933.610106443630.3468314729192.150298680480.00947421835462-0.202383236004-0.2842651794550.18638259062-0.0834039079480.4615325035820.446551928756-0.0942770095897-0.003167210635880.3557664075860.008261475843690.04357727760790.4196034003740.04333482327630.372817818471-25.20638936913.7372905776-9.1214612233
61.19686664650.8360997570170.1402566514112.4935360517-0.4531339500122.264212440610.0589176273602-0.170371908364-0.214927136357-0.1676943150170.0263770572711-0.2373578320250.3144479577610.240746613103-0.06240430656950.309065878220.005591327300070.001476122299840.454704240042-0.03823948551010.341086789589-14.99765168659.1279788995-14.8360093535
71.45208161035-0.1779599546160.3209633569961.08750530049-0.03633654772032.50025837998-0.02562589839490.003111337837280.0420043174437-0.04995670875980.0407712048546-0.1195472830590.004910932631910.256433547551-0.02102906082240.222589815774-0.03002468467320.02786942331250.302702555738-0.03483890976140.279171546531-16.798170948216.6967494762-31.6191281956
83.50503293252-0.314465265580.09633842317332.106171465430.05830961104322.88953266301-0.197557966685-0.905201206165-0.4582201768580.5005983496350.29567237848-0.4169866636620.3028334341550.687401164242-0.1022925607630.5087231510170.1371770463420.07015316830910.7924409475650.005496690707280.533471199228-29.333343238921.534428990326.9283712514
91.70679445003-0.341248388734-0.4193958306942.157478526540.0261608839342.641181133460.0256997637328-0.1992811022290.2224893265810.1333568508370.0683082835773-0.109354024706-0.3503279683020.132391351845-0.1098666563040.3268001200120.005595123280620.1117911985740.476344015353-0.03936391427920.388074509103-34.277210568929.4209471616.2246050325
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 193 )AA130 - 193112 - 175
44chain 'A' and (resid 194 through 293 )AA194 - 293176 - 275
55chain 'A' and (resid 294 through 384 )AA294 - 384276 - 366
66chain 'A' and (resid 385 through 431 )AA385 - 431367 - 413
77chain 'A' and (resid 432 through 614 )AA432 - 614414 - 596
88chain 'B' and (resid 333 through 421 )BI333 - 4211 - 89
99chain 'B' and (resid 422 through 527 )BI422 - 52790 - 195

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