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- PDB-8xi6: SARS-CoV-2 Omicron BQ.1.1 Variant Spike Protein Complexed with MO... -

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Basic information

Entry
Database: PDB / ID: 8xi6
TitleSARS-CoV-2 Omicron BQ.1.1 Variant Spike Protein Complexed with MO11 Fab
Components
  • MO11 heavy chain
  • MO11 light chain
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 ...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 / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsIshimaru, H. / Nishimura, M. / Shigematsu, H. / Marini, M.I. / Hasegawa, N. / Takamiya, R. / Iwata, S. / Mori, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Virol / Year: 2024
Title: Epitopes of an antibody that neutralizes a wide range of SARS-CoV-2 variants in a conserved subdomain 1 of the spike protein.
Authors: Hanako Ishimaru / Mitsuhiro Nishimura / Hideki Shigematsu / Maria Istiqomah Marini / Natsumi Hasegawa / Rei Takamiya / Sachiyo Iwata / Yasuko Mori /
Abstract: The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued, enabling the virus to escape from host immunity by changing its spike antigen, while biased toward the ...The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued, enabling the virus to escape from host immunity by changing its spike antigen, while biased toward the receptor-binding domain and N-terminal domain. Here, we isolated a novel pan-SARS-CoV-2 neutralizing antibody (which we named MO11) for even the recent dominators XBB.1.16 and EG.5.1, from a convalescent patient who had received three doses of an original mRNA COVID-19 vaccination. A cryo-electron microscopy analysis of the spike-MO11 complex at 2.3 Å atomic resolution revealed that it recognizes a conserved epitope hidden behind a glycan shield at N331 on subdomain 1 (SD1), holding both the N- and C-terminal segments comprising SD1. Our identification of MO11 unveiled the functional importance of SD1 for the spike's function, and we discuss the potential availability of a novel common epitope among the SARS-CoV-2 variants.IMPORTANCENovel severe acute respiratory syndrome coronavirus 2 variants with immune evasion ability are still repeatedly emerging, nonetheless, a part of immunity developed in responding to the antigen of earlier variants retains efficacy against recent variants irrespective of the numerous mutations. In exploration for the broadly effective antibodies, we identified a cross-neutralizing antibody, named MO11, from the B cells of the convalescent patient. MO11 targets a novel epitope in subdomain 1 (SD1) and was effective against all emerging variants including XBB.1.16 and EG.5.1. The neutralizing activity covering from D614G to EG.5.1 variants was explained by the conservation of the epitope, and it revealed the importance of the subdomain on regulating the function of the antigen for viral infection. Demonstrated identification of the neutralizing antibody that recognizes a conserved epitope implies basal contribution of such group of antibodies for prophylaxis against COVID-19.
History
DepositionDec 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _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: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
D: MO11 heavy chain
E: MO11 light chain
F: MO11 heavy chain
G: MO11 light chain
H: MO11 heavy chain
I: MO11 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)570,71045
Polymers558,3359
Non-polymers12,37536
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_1ens_2chain "F"
d_2ens_2chain "D"
d_3ens_2chain "H"
d_1ens_3chain "E"
d_2ens_3chain "G"
d_3ens_3chain "I"

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_1GLNGLNLEULEUBB26 - 114123 - 1133
d_12ens_1NAGNAGNAGNAGOO1
d_13ens_1NAGNAGNAGNAGPP1
d_14ens_1NAGNAGNAGNAGQQ1
d_15ens_1NAGNAGNAGNAGBFA1301
d_16ens_1NAGNAGNAGNAGRR1
d_17ens_1NAGNAGNAGNAGRR2
d_18ens_1NAGNAGNAGNAGBGA1302
d_19ens_1NAGNAGNAGNAGSS1
d_110ens_1NAGNAGNAGNAGBHA1303
d_111ens_1NAGNAGNAGNAGBIA1304
d_112ens_1NAGNAGNAGNAGBJA1305
d_113ens_1NAGNAGNAGNAGBKA1306
d_114ens_1FUCFUCFUCFUCRR4
d_115ens_1NAGNAGNAGNAGSS2
d_116ens_1FUCFUCFUCFUCSS3
d_117ens_1BMABMABMABMARR3
d_118ens_1NAGNAGNAGNAGPP2
d_119ens_1NAGNAGNAGNAGOO2
d_120ens_1NAGNAGNAGNAGQQ2
d_121ens_1NAGNAGNAGNAGBLA1307
d_21ens_1GLNGLNLEULEUAA26 - 114123 - 1133
d_22ens_1NAGNAGNAGNAGJJ1
d_23ens_1NAGNAGNAGNAGKK1
d_24ens_1NAGNAGNAGNAGLL1
d_25ens_1NAGNAGNAGNAGAY1301
d_26ens_1NAGNAGNAGNAGMM1
d_27ens_1NAGNAGNAGNAGMM2
d_28ens_1NAGNAGNAGNAGAZ1302
d_29ens_1NAGNAGNAGNAGNN1
d_210ens_1NAGNAGNAGNAGAAA1303
d_211ens_1NAGNAGNAGNAGABA1304
d_212ens_1NAGNAGNAGNAGACA1305
d_213ens_1NAGNAGNAGNAGADA1306
d_214ens_1FUCFUCFUCFUCMM4
d_215ens_1NAGNAGNAGNAGNN2
d_216ens_1FUCFUCFUCFUCNN3
d_217ens_1BMABMABMABMAMM3
d_218ens_1NAGNAGNAGNAGKK2
d_219ens_1NAGNAGNAGNAGJJ2
d_220ens_1NAGNAGNAGNAGLL2
d_221ens_1NAGNAGNAGNAGAEA1307
d_31ens_1GLNGLNLEULEUCC26 - 114123 - 1133
d_32ens_1NAGNAGNAGNAGTT1
d_33ens_1NAGNAGNAGNAGUU1
d_34ens_1NAGNAGNAGNAGVV1
d_35ens_1NAGNAGNAGNAGCMA1301
d_36ens_1NAGNAGNAGNAGWW1
d_37ens_1NAGNAGNAGNAGWW2
d_38ens_1NAGNAGNAGNAGCNA1302
d_39ens_1NAGNAGNAGNAGXX1
d_310ens_1NAGNAGNAGNAGCOA1303
d_311ens_1NAGNAGNAGNAGCPA1304
d_312ens_1NAGNAGNAGNAGCQA1305
d_313ens_1NAGNAGNAGNAGCRA1306
d_314ens_1FUCFUCFUCFUCWW4
d_315ens_1NAGNAGNAGNAGXX2
d_316ens_1FUCFUCFUCFUCXX3
d_317ens_1BMABMABMABMAWW3
d_318ens_1NAGNAGNAGNAGUU2
d_319ens_1NAGNAGNAGNAGTT2
d_320ens_1NAGNAGNAGNAGVV2
d_321ens_1NAGNAGNAGNAGCSA1307
d_11ens_2GLUGLUVALVALFF1 - 1111 - 123
d_21ens_2GLUGLUVALVALDD1 - 1111 - 123
d_31ens_2GLUGLUVALVALHH1 - 1111 - 123
d_11ens_3TYRTYRLEULEUEE3 - 1042 - 105
d_21ens_3TYRTYRLEULEUGG3 - 1042 - 105
d_31ens_3TYRTYRLEULEUII3 - 1042 - 105

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.500143544623, 0.865942511789, -3.23759229966E-5), (-0.86594250534, -0.500143544971, -0.000108947220383), (-0.00011053463857, -2.64535611067E-5, 0.999999993541)114.46386218, 427.055895335, 0.0234769162339
2given(-0.499900261789, -0.866082979776, 2.0142083871E-5), (0.866082970068, -0.499900252391, 0.0001631464097), (-0.000131229295842, 9.90016487413E-5, 0.999999986489)427.013869864, 114.364014019, 0.00387024150467
3given(-0.501649926082, 0.865070694859, -0.000211088051796), (-0.865069501113, -0.50164961369, -0.00155670471675), (-0.00145255187064, -0.000598314970429, 0.999998766055)114.835967634, 427.443764767, 0.288716903496
4given(-0.499869191669, -0.866100866698, -0.000282710146853), (0.866100754089, -0.499868875783, -0.000768628946369), (0.00052439219334, -0.000629069401493, 0.999999664642)427.077265356, 114.549294529, 0.0163303159067
5given(-0.499306322691, -0.866425446542, -0.000376438222643), (0.866425297895, -0.499306459642, 0.000512375275977), (-0.000631893013507, -7.03233843064E-5, 0.999999797883)427.064091871, 114.058602386, 0.11768789425
6given(-0.500147793406, 0.865939754121, -0.000725936871031), (-0.865939945272, -0.500147980841, -9.18864622361E-5), (-0.00044264400078, 0.00058266092304, 0.999999732286)114.601578795, 427.060320587, -0.0636744677492

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 138784.125 Da / Num. of mol.: 3 / Mutation: F817P, A892P, A899P, A942P, K986P, V987P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Strain: TY41-796 / Gene: S, 2 / Variant: BQ.1.1 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

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Antibody , 2 types, 6 molecules DFHEGI

#2: Antibody MO11 heavy chain


Mass: 24479.309 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody MO11 light chain


Mass: 22848.344 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 4 types, 36 molecules

#4: 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.: 9
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
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 21 / 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

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Details

Has ligand of interestY
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: Complex of spike ectodomain with antibody MO11 Fab / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.5 MDa / Experimental value: NO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
120 mMTris-HCl1
2150 mMNaCl1
SpecimenConc.: 8.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO1.8.2particle selection
2SerialEM4.1beta10image acquisition
4CTFFIND4.1CTF correction
7UCSF ChimeraX1.6model fitting
9PHENIX1.21rc1_5109model refinement
10Coot0.9.8.1model refinement
11RELION4.0.0initial Euler assignment
12RELION4.0.0final Euler assignment
14RELION4.0.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 246238 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18H3N

8h3n

18H3N1PDBexperimental model
21AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 65.25 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00229940
ELECTRON MICROSCOPYf_angle_d0.518640791
ELECTRON MICROSCOPYf_chiral_restr0.04514800
ELECTRON MICROSCOPYf_plane_restr0.00425181
ELECTRON MICROSCOPYf_dihedral_angle_d3.78333875
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BBELECTRON MICROSCOPYNCS constraints8.51927743878E-13
ens_1d_3BBELECTRON MICROSCOPYNCS constraints2.59462864664E-13
ens_2d_2FFELECTRON MICROSCOPYNCS constraints5.06257205223E-13
ens_2d_3FFELECTRON MICROSCOPYNCS constraints1.52913565428E-10
ens_3d_2EEELECTRON MICROSCOPYNCS constraints6.25732774063E-11
ens_3d_3EEELECTRON MICROSCOPYNCS constraints2.46517814029E-12

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