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- PDB-7wpf: SARS-CoV-2 Omicron Variant S Trimer complexed with three JMB2002 Fab -

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Basic information

Entry
Database: PDB / ID: 7wpf
TitleSARS-CoV-2 Omicron Variant S Trimer complexed with three JMB2002 Fab
Components
  • Anti-Fab nanobody
  • JMB2002 Fab heavy chain
  • JMB2002 Fab light chain
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / Antibody
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 / 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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Mus musculus (house mouse)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsYin, W. / Xu, Y. / Xu, P. / Cao, X. / Wu, C. / Gu, C. / He, X. / Wang, X. / Huang, S. / Yuan, Q. ...Yin, W. / Xu, Y. / Xu, P. / Cao, X. / Wu, C. / Gu, C. / He, X. / Wang, X. / Huang, S. / Yuan, Q. / Wu, K. / Hu, W. / Huang, Z. / Liu, J. / Wang, Z. / Jia, F. / Xia, K. / Liu, P. / Wang, X. / Song, B. / Zheng, J. / Jiang, H. / Cheng, X. / Jiang, Y. / Deng, S.J. / Xu, H.E.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81902085 China
CitationJournal: Science / Year: 2022
Title: Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody.
Authors: Wanchao Yin / Youwei Xu / Peiyu Xu / Xiaodan Cao / Canrong Wu / Chunyin Gu / Xinheng He / Xiaoxi Wang / Sijie Huang / Qingning Yuan / Kai Wu / Wen Hu / Zifu Huang / Jia Liu / Zongda Wang / ...Authors: Wanchao Yin / Youwei Xu / Peiyu Xu / Xiaodan Cao / Canrong Wu / Chunyin Gu / Xinheng He / Xiaoxi Wang / Sijie Huang / Qingning Yuan / Kai Wu / Wen Hu / Zifu Huang / Jia Liu / Zongda Wang / Fangfang Jia / Kaiwen Xia / Peipei Liu / Xueping Wang / Bin Song / Jie Zheng / Hualiang Jiang / Xi Cheng / Yi Jiang / Su-Jun Deng / H Eric Xu /
Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has become the dominant infective strain. We report the structures of the Omicron spike trimer on its own and in ...The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has become the dominant infective strain. We report the structures of the Omicron spike trimer on its own and in complex with angiotensin-converting enzyme 2 (ACE2) or an anti-Omicron antibody. Most Omicron mutations are located on the surface of the spike protein and change binding epitopes to many current antibodies. In the ACE2-binding site, compensating mutations strengthen receptor binding domain (RBD) binding to ACE2. Both the RBD and the apo form of the Omicron spike trimer are thermodynamically unstable. An unusual RBD-RBD interaction in the ACE2-spike complex supports the open conformation and further reinforces ACE2 binding to the spike trimer. A broad-spectrum therapeutic antibody, JMB2002, which has completed a phase 1 clinical trial, maintains neutralizing activity against Omicron. JMB2002 binds to RBD differently from other characterized antibodies and inhibits ACE2 binding.
History
DepositionJan 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
R: JMB2002 Fab heavy chain
S: JMB2002 Fab light chain
T: Anti-Fab nanobody
U: JMB2002 Fab heavy chain
V: JMB2002 Fab light chain
W: Anti-Fab nanobody
X: JMB2002 Fab heavy chain
Y: JMB2002 Fab light chain
Z: Anti-Fab nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)599,91549
Polymers591,32412
Non-polymers8,59137
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area49920 Å2
ΔGint-101 kcal/mol
Surface area211050 Å2

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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: 133911.969 Da / Num. of mol.: 3 / Mutation: Q498R, R682G, R683S, R685S, K986P, V987P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Variant: omicron / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

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Antibody , 3 types, 9 molecules RUXSVYTWZ

#2: Antibody JMB2002 Fab heavy chain


Mass: 25218.160 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody JMB2002 Fab light chain


Mass: 23331.854 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Antibody Anti-Fab nanobody


Mass: 14645.946 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Sugars , 2 types, 37 molecules

#5: 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.: 2
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
#6: 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.: 35
Source method: isolated from a genetically manipulated source
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 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 Omicron Variant S Trimer complexed with JMB2002 FabCOMPLEX#1-#40RECOMBINANT
2SARS-CoV-2 Omicron Variant SCOMPLEX#11RECOMBINANT
3JMB2002 FabCOMPLEX#2-#31RECOMBINANT
4Anti Fab nanobodyCOMPLEX#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Severe acute respiratory syndrome coronavirus 22697049
32Mus musculus (house mouse)10090
43Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606HEK293
32Trichoplusia ni (cabbage looper)7111
43Homo sapiens (human)9606HEK293
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 22000 nm / Nominal defocus min: 12000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
Image processingDetails: The SARS-CoV-2 Omicron S trimer-JMB2002 Fab complex was assembled by incubation.
CTF correctionType: NONE
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 434893 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00237390
ELECTRON MICROSCOPYf_angle_d0.59750985
ELECTRON MICROSCOPYf_dihedral_angle_d29.95364
ELECTRON MICROSCOPYf_chiral_restr0.0885962
ELECTRON MICROSCOPYf_plane_restr0.0046537

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