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- PDB-8vko: Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex ... -

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Basic information

Entry
Database: PDB / ID: 8vko
TitleCryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with human ACE2
Components
  • Processed angiotensin-converting enzyme 2
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM 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 / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsZhu, X. / Mannar, D. / Saville, J. / Poloni, C. / Bezeruk, A. / Tidey, K. / Ahmed, S. / Tuttle, K. / Vahdatihassani, F. / Cholak, S. ...Zhu, X. / Mannar, D. / Saville, J. / Poloni, C. / Bezeruk, A. / Tidey, K. / Ahmed, S. / Tuttle, K. / Vahdatihassani, F. / Cholak, S. / Cook, L. / Steiner, T.S. / Subramaniam, S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canada Excellence Research Chair Award Canada
CitationJournal: Nat Commun / Year: 2024
Title: Altered receptor binding, antibody evasion and retention of T cell recognition by the SARS-CoV-2 XBB.1.5 spike protein.
Authors: Dhiraj Mannar / James W Saville / Chad Poloni / Xing Zhu / Alison Bezeruk / Keith Tidey / Sana Ahmed / Katharine S Tuttle / Faezeh Vahdatihassani / Spencer Cholak / Laura Cook / Theodore S ...Authors: Dhiraj Mannar / James W Saville / Chad Poloni / Xing Zhu / Alison Bezeruk / Keith Tidey / Sana Ahmed / Katharine S Tuttle / Faezeh Vahdatihassani / Spencer Cholak / Laura Cook / Theodore S Steiner / Sriram Subramaniam /
Abstract: The XBB.1.5 variant of SARS-CoV-2 has rapidly achieved global dominance and exhibits a high growth advantage over previous variants. Preliminary reports suggest that the success of XBB.1.5 stems from ...The XBB.1.5 variant of SARS-CoV-2 has rapidly achieved global dominance and exhibits a high growth advantage over previous variants. Preliminary reports suggest that the success of XBB.1.5 stems from mutations within its spike glycoprotein, causing immune evasion and enhanced receptor binding. We present receptor binding studies that demonstrate retention of binding contacts with the human ACE2 receptor and a striking decrease in binding to mouse ACE2 due to the revertant R493Q mutation. Despite extensive evasion of antibody binding, we highlight a region on the XBB.1.5 spike protein receptor binding domain (RBD) that is recognized by serum antibodies from a donor with hybrid immunity, collected prior to the emergence of the XBB.1.5 variant. T cell assays reveal high frequencies of XBB.1.5 spike-specific CD4 and CD8 T cells amongst donors with hybrid immunity, with the CD4 T cells skewed towards a Th1 cell phenotype and having attenuated effector cytokine secretion as compared to ancestral spike protein-specific cells. Thus, while the XBB.1.5 variant has retained efficient human receptor binding and gained antigenic alterations, it remains susceptible to recognition by T cells induced via vaccination and previous infection.
History
DepositionJan 9, 2024Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
D: Processed angiotensin-converting enzyme 2
E: Processed angiotensin-converting enzyme 2
F: Processed angiotensin-converting enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)655,32663
Polymers637,8416
Non-polymers17,48557
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_1ens_2chain "D"
d_2ens_2chain "E"
d_3ens_2chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLNGLNSERSERAA14 - 114714 - 1143
d_12ens_1NAGNAGNAGNAGAEA1301
d_13ens_1NAGNAGNAGNAGGG1
d_14ens_1NAGNAGNAGNAGGG2
d_15ens_1NAGNAGNAGNAGAFA1302
d_16ens_1NAGNAGNAGNAGAGA1303
d_17ens_1NAGNAGNAGNAGAHA1304
d_18ens_1NAGNAGNAGNAGAIA1305
d_19ens_1NAGNAGNAGNAGAJA1306
d_110ens_1NAGNAGNAGNAGAKA1307
d_111ens_1NAGNAGNAGNAGHH1
d_112ens_1NAGNAGNAGNAGHH2
d_113ens_1NAGNAGNAGNAGII1
d_114ens_1NAGNAGNAGNAGII2
d_115ens_1NAGNAGNAGNAGJJ1
d_116ens_1NAGNAGNAGNAGJJ2
d_117ens_1NAGNAGNAGNAGKK1
d_118ens_1NAGNAGNAGNAGKK2
d_119ens_1NAGNAGNAGNAGLL1
d_120ens_1NAGNAGNAGNAGLL2
d_21ens_1GLNGLNSERSERBB14 - 114714 - 1143
d_22ens_1NAGNAGNAGNAGBLA1301
d_23ens_1NAGNAGNAGNAGMM1
d_24ens_1NAGNAGNAGNAGMM2
d_25ens_1NAGNAGNAGNAGBMA1302
d_26ens_1NAGNAGNAGNAGBNA1303
d_27ens_1NAGNAGNAGNAGBOA1304
d_28ens_1NAGNAGNAGNAGBPA1305
d_29ens_1NAGNAGNAGNAGBQA1306
d_210ens_1NAGNAGNAGNAGBRA1307
d_211ens_1NAGNAGNAGNAGNN1
d_212ens_1NAGNAGNAGNAGNN2
d_213ens_1NAGNAGNAGNAGOO1
d_214ens_1NAGNAGNAGNAGOO2
d_215ens_1NAGNAGNAGNAGPP1
d_216ens_1NAGNAGNAGNAGPP2
d_217ens_1NAGNAGNAGNAGQQ1
d_218ens_1NAGNAGNAGNAGQQ2
d_219ens_1NAGNAGNAGNAGRR1
d_220ens_1NAGNAGNAGNAGRR2
d_31ens_1GLNGLNSERSERCC14 - 114714 - 1143
d_32ens_1NAGNAGNAGNAGCSA1301
d_33ens_1NAGNAGNAGNAGSS1
d_34ens_1NAGNAGNAGNAGSS2
d_35ens_1NAGNAGNAGNAGCTA1302
d_36ens_1NAGNAGNAGNAGCUA1303
d_37ens_1NAGNAGNAGNAGCVA1304
d_38ens_1NAGNAGNAGNAGCWA1305
d_39ens_1NAGNAGNAGNAGCXA1306
d_310ens_1NAGNAGNAGNAGCYA1307
d_311ens_1NAGNAGNAGNAGTT1
d_312ens_1NAGNAGNAGNAGTT2
d_313ens_1NAGNAGNAGNAGUU1
d_314ens_1NAGNAGNAGNAGUU2
d_315ens_1NAGNAGNAGNAGVV1
d_316ens_1NAGNAGNAGNAGVV2
d_317ens_1NAGNAGNAGNAGWW1
d_318ens_1NAGNAGNAGNAGWW2
d_319ens_1NAGNAGNAGNAGXX1
d_320ens_1NAGNAGNAGNAGXX2
d_11ens_2SERSERTYRTYRDD19 - 6132 - 596
d_12ens_2NAGNAGNAGNAGDZA701
d_13ens_2NAGNAGNAGNAGDAB702
d_14ens_2NAGNAGNAGNAGYY1
d_15ens_2NAGNAGNAGNAGYY2
d_16ens_2NAGNAGNAGNAGDBB703
d_17ens_2NAGNAGNAGNAGDCB704
d_18ens_2NAGNAGNAGNAGZZ1
d_19ens_2NAGNAGNAGNAGZZ2
d_21ens_2SERSERTYRTYREE19 - 6132 - 596
d_22ens_2NAGNAGNAGNAGEDB701
d_23ens_2NAGNAGNAGNAGEEB702
d_24ens_2NAGNAGNAGNAGaAA1
d_25ens_2NAGNAGNAGNAGaAA2
d_26ens_2NAGNAGNAGNAGEFB703
d_27ens_2NAGNAGNAGNAGEGB704
d_28ens_2NAGNAGNAGNAGbBA1
d_29ens_2NAGNAGNAGNAGbBA2
d_31ens_2SERSERTYRTYRFF19 - 6132 - 596
d_32ens_2NAGNAGNAGNAGFHB701
d_33ens_2NAGNAGNAGNAGFIB702
d_34ens_2NAGNAGNAGNAGcCA1
d_35ens_2NAGNAGNAGNAGcCA2
d_36ens_2NAGNAGNAGNAGFJB703
d_37ens_2NAGNAGNAGNAGFKB704
d_38ens_2NAGNAGNAGNAGdDA1
d_39ens_2NAGNAGNAGNAGdDA2

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.50336362798, -0.864073921923, 0.00114694360326), (0.864058496441, -0.503345630356, 0.00678904477754), (-0.00528892749607, 0.00440838457508, 0.999976296415)473.453381593, 126.847533957, 0.0545061820246
2given(-0.498993446892, 0.866588655484, -0.00544446010561), (-0.866583233823, -0.499015925922, -0.00407486597413), (-0.00624810492654, 0.00268474642669, 0.999976876393)127.390840044, 473.724679105, 0.648732893092
3given(-0.503363543272, -0.864073970935, 0.00114719559903), (0.86405854758, -0.503345545165, 0.00678885237302), (-0.00528863483384, 0.00440850494832, 0.999976297432)473.453310481, 126.847564455, 0.0544276371224
4given(-0.49899353953, 0.866588602075, -0.00544447076591), (-0.866583180318, -0.499016018678, -0.00407488554457), (-0.0062481274931, 0.00268474523041, 0.999976876256)127.390880581, 473.724679887, 0.648741050087

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Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 142226.516 Da / Num. of mol.: 3
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
#2: Protein Processed angiotensin-converting enzyme 2


Mass: 70386.992 Da / Num. of mol.: 3
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
#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.: 24
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
#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.: 33 / 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
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SARS-CoV-2 XBB.1.5 spike protein trimer bound to 3 human ACE2 molecules
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50498 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 113.65 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004641283
ELECTRON MICROSCOPYf_angle_d0.876856145
ELECTRON MICROSCOPYf_chiral_restr0.05456414
ELECTRON MICROSCOPYf_plane_restr0.00697152
ELECTRON MICROSCOPYf_dihedral_angle_d13.59114961
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints8.83252243408E-12
ens_1d_3AAELECTRON MICROSCOPYNCS constraints9.16768239786E-13
ens_2d_2DDELECTRON MICROSCOPYNCS constraints7.52818210863E-11
ens_2d_3DDELECTRON MICROSCOPYNCS constraints2.50743232982E-10

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