ISDA

Deposition Date 2024-02-21

Release Date 2025-01-15

Last Version Date 2025-01-15

Entry Detail

PDB ID:

8YDX

Keywords:

VIRAL PROTEIN/INHIBITOR

Title:

Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.2 variant) in complex with CeSPIACE

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)
synthetic construct (Taxon ID: 32630)

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

4.90 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spike glycoprotein
Gene (Uniprot):S
Mutations:F817P, A892P, A898P, A942P, K986P, V987P
Chain IDs:D (auth: C), E (auth: B), F (auth: A)
Chain Length:1307
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF16451, PF09408, PF19209, PF01601

Polymer Type:polypeptide(L)
Molecule:CeSPIACE
Chain IDs:A (auth: D), B (auth: F), C (auth: E)
Chain Length:39
Number of Molecules:3
Biological Source:synthetic construct

Ligand Molecules

NAG

Primary Citation

Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology

Nakamura, S, Tanimura, Y, Nomura, R, Suzuki, H, Nishikawa, K, Kamegawa, A, Numoto, N, Tanaka, A, Kawabata, S, Sakaguchi, S, Emi, A, Suzuki, Y, Fujiyoshi, Y.Show

To Be Published ? ? ? (?)

Primary Citation of related structures