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- PDB-8hgm: Structure of SARS-CoV-2 spike RBD in complex with neutralizing an... -

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Basic information

Entry
Database: PDB / ID: 8hgm
TitleStructure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-11
Components
  • NIV-11 Fab heavy chain
  • NIV-11 Fab light chain
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / Induction of Cell-Cell Fusion / structural constituent of virion ...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 / Induction of Cell-Cell Fusion / 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 / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 / 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, 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 ...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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMoriyama, S. / Anraku, Y. / Muranishi, S. / Adachi, Y. / Kuroda, D. / Higuchi, Y. / Kotaki, R. / Tonouchi, K. / Yumoto, K. / Suzuki, T. ...Moriyama, S. / Anraku, Y. / Muranishi, S. / Adachi, Y. / Kuroda, D. / Higuchi, Y. / Kotaki, R. / Tonouchi, K. / Yumoto, K. / Suzuki, T. / Kita, S. / Someya, T. / Fukuhara, H. / Kuroda, Y. / Yamamoto, T. / Onodera, T. / Fukushi, S. / Maeda, K. / Nakamura-Uchiyama, F. / Hashiguchi, T. / Hoshino, A. / Maenaka, K. / Takahashi, Y.
Funding support Japan, 10items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20fk0108516 Japan
Japan Agency for Medical Research and Development (AMED)JP21fk0108465 Japan
Japan Agency for Medical Research and Development (AMED)JP20fk0108298 Japan
Japan Agency for Medical Research and Development (AMED)JP20fk0108534 Japan
Japan Agency for Medical Research and Development (AMED)JP21fk0108534 Japan
Japan Agency for Medical Research and Development (AMED)JP19fk0108104 Japan
Japan Agency for Medical Research and Development (AMED)JP20fk0108104 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121037 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05873 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05773 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Authors: Saya Moriyama / Yuki Anraku / Shunta Taminishi / Yu Adachi / Daisuke Kuroda / Shunsuke Kita / Yusuke Higuchi / Yuhei Kirita / Ryutaro Kotaki / Keisuke Tonouchi / Kohei Yumoto / Tateki Suzuki ...Authors: Saya Moriyama / Yuki Anraku / Shunta Taminishi / Yu Adachi / Daisuke Kuroda / Shunsuke Kita / Yusuke Higuchi / Yuhei Kirita / Ryutaro Kotaki / Keisuke Tonouchi / Kohei Yumoto / Tateki Suzuki / Taiyou Someya / Hideo Fukuhara / Yudai Kuroda / Tsukasa Yamamoto / Taishi Onodera / Shuetsu Fukushi / Ken Maeda / Fukumi Nakamura-Uchiyama / Takao Hashiguchi / Atsushi Hoshino / Katsumi Maenaka / Yoshimasa Takahashi /
Abstract: SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies ...SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies resilient to mutations in emerging Omicron subvariants. Y489 was identified as a site of virus vulnerability and a common footprint of broadly neutralizing antibodies against the subvariants. Multiple Y489-binding antibodies were encoded by public clonotypes and additionally recognized F486, potentially accounting for the emergence of Omicron subvariants harboring the F486V mutation. However, a subclass of antibodies broadly neutralized BA.4/BA.5 variants via hydrophobic binding sites of rare clonotypes along with high mutation-resilience under escape mutation screening. A computationally designed antibody based on one of the Y489-binding antibodies, NIV-10/FD03, was able to bind XBB with any 486 mutation and neutralized XBB.1.5. The structural basis for the mutation-resilience of this Y489-binding antibody group may provide important insights into the design of therapeutics resistant to viral escape.
History
DepositionNov 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Structure summary / Category: audit_author / em_author_list
Revision 1.2Sep 25, 2024Group: Data collection / Source and taxonomy / Category: em_admin / em_entity_assembly_recombinant
Item: _em_admin.last_update / _em_entity_assembly_recombinant.id
Revision 1.3Nov 6, 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
B: Spike glycoprotein
C: NIV-11 Fab heavy chain
D: NIV-11 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,1614
Polymers189,7363
Non-polymers4241
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Spike glycoprotein


Mass: 142427.438 Da / Num. of mol.: 1
Mutation: R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody NIV-11 Fab heavy chain


Mass: 23753.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody NIV-11 Fab light chain


Mass: 23555.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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.: 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
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

Component
IDNameTypeEntity IDParent-IDSource
1SARS-COV-2 spike glycoprotein in complex with NIV-11COMPLEX#1-#30RECOMBINANT
2SARS-CoV-2 spike glycoproteinCOMPLEX#11RECOMBINANT
3NIV-11 FabCOMPLEX#2-#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.57 MDaNO
220.42 MDaNO
330.05 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Severe acute respiratory syndrome coronavirus 22697049
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Buffer solutionpH: 7.4
Details: octyl-maltoside, fluorinated solution was added to PBS solution to a final concentration of 0.03%
SpecimenConc.: 1 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 R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K / Details: blotting time 5 s and blotting force 5.

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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 magnification: 130000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 51.41 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 5170
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARC3.3.1CTF correction
7UCSF Chimera1.15model fitting
9PHENIX1.2model refinement
10cryoSPARC3.3.1initial Euler assignment
11cryoSPARC3.3.1final Euler assignment
12RELION3.1.3classification
13cryoSPARC3.3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1498301
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80132 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6M0J

6m0j


Pdb chain-ID: E / Accession code: 6M0J / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 112.92 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035007
ELECTRON MICROSCOPYf_angle_d0.5596812
ELECTRON MICROSCOPYf_dihedral_angle_d4.27702
ELECTRON MICROSCOPYf_chiral_restr0.043752
ELECTRON MICROSCOPYf_plane_restr0.004879

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