7X7N | pdb_00007x7n

3D model of the 3-RBD up single trimeric spike protein of SARS-CoV2 in the presence of synthetic peptide SIH-5.

PDB DOI: https://doi.org/10.2210/pdb7X7N/pdb
EM Map EMD-33042: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-03-10 Released: 2022-04-27
Deposition Author(s): Khatri, B., Pramanick, I., Malladi, S.K., Rajmani, R.S., Kumar, S., Ghosh, P., Sengupta, N., Rahisuddin, R., Kumaran, S., Ringe, R.P., Varadarajan, R., Dutta, S., Chatterjee, J.
Funding Organization(s): Department of Biotechnology (DBT, India), Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.47 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A dimeric proteomimetic prevents SARS-CoV-2 infection by dimerizing the spike protein.

Khatri, B., Pramanick, I., Malladi, S.K., Rajmani, R.S., Kumar, S., Ghosh, P., Sengupta, N., Rahisuddin, R., Kumar, N., Kumaran, S., Ringe, R.P., Varadarajan, R., Dutta, S., Chatterjee, J.

(2022) Nat Chem Biol 18: 1046-1055

PubMed: 35654847 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41589-022-01060-0
Primary Citation Related Structures:
7X7N

PubMed Abstract:
Protein tertiary structure mimetics are valuable tools to target large protein-protein interaction interfaces. Here, we demonstrate a strategy for designing dimeric helix-hairpin motifs from a previously reported three-helix-bundle miniprotein that targets the receptor-binding domain (RBD) of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Through truncation of the third helix and optimization of the interhelical loop residues of the miniprotein, we developed a thermostable dimeric helix-hairpin. The dimeric four-helix bundle competes with the human angiotensin-converting enzyme 2 (ACE2) in binding to RBD with 2:2 stoichiometry. Cryogenic-electron microscopy revealed the formation of dimeric spike ectodomain trimer by the four-helix bundle, where all the three RBDs from either spike protein are attached head-to-head in an open conformation, revealing a novel mechanism for virus neutralization. The proteomimetic protects hamsters from high dose viral challenge with replicative SARS-CoV-2 viruses, demonstrating the promise of this class of peptides that inhibit protein-protein interaction through target dimerization.

Organizational Affiliation

Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India.

Macromolecule Content

Total Structure Weight: 463.76 kDa
Atom Count: 26,493
Modeled Residue Count: 3,320
Deposited Residue Count: 4,092
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B], B [auth C], C [auth A]	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 5 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 13	Glycosylation Focus chain A [auth B] Focus chain B [auth C] Focus chain C [auth A]	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic peptide SIH-5	D E F [auth H] G [auth I] H [auth F] D, E, F [auth H], G [auth I], H [auth F], I [auth G]	38	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain VA [auth A] SDF format, chain V [auth B] SDF format, chain UA [auth A] SDF format, chain U [auth B] SDF format, chain TA [auth A] SDF format, chain T [auth B] SDF format, chain SA [auth A] SDF format, chain S [auth B] SDF format, chain RA [auth A] SDF format, chain R [auth B] SDF format, chain QA [auth A] SDF format, chain Q [auth B] SDF format, chain PA [auth A] SDF format, chain P [auth B] SDF format, chain OA [auth A] SDF format, chain O [auth B] SDF format, chain NA [auth A] SDF format, chain N [auth B] SDF format, chain MA [auth A] SDF format, chain M [auth B] SDF format, chain LA [auth A] SDF format, chain L [auth B] SDF format, chain KA [auth A] SDF format, chain K [auth B] SDF format, chain JA [auth A] SDF format, chain J [auth B] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain VA [auth A] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth A] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth A] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth A] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth A] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth A] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth A] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth A] MOL2 format, chain N [auth B] MOL2 format, chain MA [auth A] MOL2 format, chain M [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain L [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain K [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain J [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain VA [auth A] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth A] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth A] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth A] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth A] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth A] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth A] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth A] mmCIF format, chain N [auth B] mmCIF format, chain MA [auth A] mmCIF format, chain M [auth B] mmCIF format, chain LA [auth A] mmCIF format, chain L [auth B] mmCIF format, chain KA [auth A] mmCIF format, chain K [auth B] mmCIF format, chain JA [auth A] mmCIF format, chain J [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth C] AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], J [auth B], JA [auth A], K [auth B], KA [auth A], L [auth B], LA [auth A], M [auth B], MA [auth A], N [auth B], NA [auth A], O [auth B], OA [auth A], P [auth B], PA [auth A], Q [auth B], QA [auth A], R [auth B], RA [auth A], S [auth B], SA [auth A], T [auth B], TA [auth A], U [auth B], UA [auth A], V [auth B], VA [auth A], W [auth C], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth B] Focus chain JA [auth A] Focus chain K [auth B] Focus chain KA [auth A] Focus chain L [auth B] Focus chain LA [auth A] Focus chain M [auth B] Focus chain MA [auth A] Focus chain N [auth B] Focus chain NA [auth A] Focus chain O [auth B] Focus chain OA [auth A] Focus chain P [auth B] Focus chain PA [auth A] Focus chain Q [auth B] Focus chain QA [auth A] Focus chain R [auth B] Focus chain RA [auth A] Focus chain S [auth B] Focus chain SA [auth A] Focus chain T [auth B] Focus chain TA [auth A] Focus chain U [auth B] Focus chain UA [auth A] Focus chain V [auth B] Focus chain VA [auth A] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth B] Focus chain JA [auth A] Focus chain K [auth B] Focus chain KA [auth A] Focus chain L [auth B] Focus chain LA [auth A] Focus chain M [auth B] Focus chain MA [auth A] Focus chain N [auth B] Focus chain NA [auth A] Focus chain O [auth B] Focus chain OA [auth A] Focus chain P [auth B] Focus chain PA [auth A] Focus chain Q [auth B] Focus chain QA [auth A] Focus chain R [auth B] Focus chain RA [auth A] Focus chain S [auth B] Focus chain SA [auth A] Focus chain T [auth B] Focus chain TA [auth A] Focus chain U [auth B] Focus chain UA [auth A] Focus chain V [auth B] Focus chain VA [auth A] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB Query on AIB	D E F [auth H] G [auth I] H [auth F] D, E, F [auth H], G [auth I], H [auth F], I [auth G]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
DAL Query on DAL	D E F [auth H] G [auth I] H [auth F] D, E, F [auth H], G [auth I], H [auth F], I [auth G]	D-PEPTIDE LINKING	C₃ H₇ N O₂		--