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- PDB-7zsd: cryo-EM structure of omicron spike in complex with de novo design... -

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Basic information

Entry
Database: PDB / ID: 7zsd
Titlecryo-EM structure of omicron spike in complex with de novo designed binder, local
Components
  • Spike glycoprotein
  • de novo designed binder
KeywordsANTIVIRAL PROTEIN / SARS-COV2 / de novo / design binder / spike / RBD / receptor binding domain
Function / homology
Function and homology information


positive regulation of intralumenal vesicle formation / cytoplasmic side of apical plasma membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / imaginal disc-derived wing vein morphogenesis / sensory organ precursor cell division / wing disc morphogenesis / compound eye development / female germ-line stem cell asymmetric division / phosphatidylinositol phosphate binding / sensory organ development ...positive regulation of intralumenal vesicle formation / cytoplasmic side of apical plasma membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / imaginal disc-derived wing vein morphogenesis / sensory organ precursor cell division / wing disc morphogenesis / compound eye development / female germ-line stem cell asymmetric division / phosphatidylinositol phosphate binding / sensory organ development / endosome transport via multivesicular body sorting pathway / apicolateral plasma membrane / endosomal transport / mitotic cytokinesis / negative regulation of Notch signaling pathway / Notch signaling pathway / intracellular protein transport / DNA-binding transcription repressor activity, RNA polymerase II-specific / cell cortex / Maturation of spike protein / viral translation / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / endosome membrane / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / regulation of transcription by RNA polymerase II / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Domain of unknown function DM14 / Freud, C2 domain / Coiled-coil and C2 domain-containing protein 1 / Coiled-coil and C2 domain-containing protein 1, DM14 domain / Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily ...Domain of unknown function DM14 / Freud, C2 domain / Coiled-coil and C2 domain-containing protein 1 / Coiled-coil and C2 domain-containing protein 1, DM14 domain / Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / 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 / 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 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
Spike glycoprotein / Coiled-coil and C2 domain-containing protein 1-like
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Drosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsPablo, G. / Sarah, W. / Alexandra, V.H. / Anthony, M. / Andreas, S. / Zander, H. / Dongchun, N. / Shuguang, T. / Freyr, S. / Casper, G. ...Pablo, G. / Sarah, W. / Alexandra, V.H. / Anthony, M. / Andreas, S. / Zander, H. / Dongchun, N. / Shuguang, T. / Freyr, S. / Casper, G. / Priscilla, T. / Alexandra, T. / Stephane, R. / Sandrine, G. / Jane, M. / Aaron, P. / Zepeng, X. / Yan, C. / Pu, H. / George, G. / Elisa, O. / Beat, F. / Didier, T. / Henning, S. / Michael, B. / Bruno, E.C.
Funding supportEuropean Union, Switzerland, 5items
OrganizationGrant numberCountry
European Research Council (ERC)European Research Council (starting grant no. 716058)European Union
Swiss National Science FoundationNCCR transcure 185544 Switzerland
Swiss National Science Foundation310030_188744 Switzerland
Swiss National Science FoundationNCCR Molecular Systems Engineering Switzerland
Swiss National Science FoundationNCCR Chemical Biology Switzerland
CitationJournal: Nature / Year: 2023
Title: De novo design of protein interactions with learned surface fingerprints.
Authors: Pablo Gainza / Sarah Wehrle / Alexandra Van Hall-Beauvais / Anthony Marchand / Andreas Scheck / Zander Harteveld / Stephen Buckley / Dongchun Ni / Shuguang Tan / Freyr Sverrisson / Casper ...Authors: Pablo Gainza / Sarah Wehrle / Alexandra Van Hall-Beauvais / Anthony Marchand / Andreas Scheck / Zander Harteveld / Stephen Buckley / Dongchun Ni / Shuguang Tan / Freyr Sverrisson / Casper Goverde / Priscilla Turelli / Charlène Raclot / Alexandra Teslenko / Martin Pacesa / Stéphane Rosset / Sandrine Georgeon / Jane Marsden / Aaron Petruzzella / Kefang Liu / Zepeng Xu / Yan Chai / Pu Han / George F Gao / Elisa Oricchio / Beat Fierz / Didier Trono / Henning Stahlberg / Michael Bronstein / Bruno E Correia /
Abstract: Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even ...Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This knowledge gap has been a major obstacle for the comprehensive understanding of cellular protein-protein interaction networks and for the de novo design of protein binders that are crucial for synthetic biology and translational applications. Here we use a geometric deep-learning framework operating on protein surfaces that generates fingerprints to describe geometric and chemical features that are critical to drive protein-protein interactions. We hypothesized that these fingerprints capture the key aspects of molecular recognition that represent a new paradigm in the computational design of novel protein interactions. As a proof of principle, we computationally designed several de novo protein binders to engage four protein targets: SARS-CoV-2 spike, PD-1, PD-L1 and CTLA-4. Several designs were experimentally optimized, whereas others were generated purely in silico, reaching nanomolar affinity with structural and mutational characterization showing highly accurate predictions. Overall, our surface-centric approach captures the physical and chemical determinants of molecular recognition, enabling an approach for the de novo design of protein interactions and, more broadly, of artificial proteins with function.
History
DepositionMay 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 17, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4May 24, 2023Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Spike glycoprotein
P: de novo designed binder
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5343
Polymers31,1102
Non-polymers4241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2140 Å2
ΔGint-3 kcal/mol
Surface area13950 Å2

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Components

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


Mass: 22280.193 Da / Num. of mol.: 1
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 de novo designed binder


Mass: 8829.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: l(2)gd1, lgd, CG4713 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VKJ9
#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.: 1
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
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

Component
IDNameTypeEntity IDParent-IDSource
1omicron spike in complex with de novo designed binderCOMPLEX#1-#20MULTIPLE SOURCES
2omicron spikeCOMPLEX#11RECOMBINANT
3de novo designed binderCOMPLEX#21RECOMBINANT
Molecular weightValue: 0.45 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Severe acute respiratory syndrome coronavirus 22697049
33Drosophila melanogaster (fruit fly)7227
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.82 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1820333
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50758 / Symmetry type: POINT
Atomic model buildingB value: 33.8 / Protocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 7QO7

7qo7

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032180
ELECTRON MICROSCOPYf_angle_d0.5652961
ELECTRON MICROSCOPYf_dihedral_angle_d9.638307
ELECTRON MICROSCOPYf_chiral_restr0.046314
ELECTRON MICROSCOPYf_plane_restr0.003387

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