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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 glycoproteinSpike protein
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 / 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 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: To Be Published
Title: SARS-CoV-2 XBB.1.5 Spike Protein: Altered Receptor Binding, Antibody Evasion, and Retention of T Cell Recognition
Authors: Mannar, D. / Saville, J. / Poloni, C. / Zhu, X. / Bezeruk, A. / Tidey, K. / Ahmed, S. / Tuttle, K. / Vahdatihassani, F. / Cholak, S. / Cook, L. / Steiner, T.S. / Subramaniam, S.
History
DepositionJan 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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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
Water0
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 / Spike protein / 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 / N-Acetylglucosamine


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

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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 FIELDBright-field microscopy / 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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