ISDA

Entry Detail

PDB ID:

8YDZ

EMDB ID:

EMD-39186

Keywords:

VIRAL PROTEIN/INHIBITOR

Title:

Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.5 variant) in complex with CeSPIACE, class 2

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2, synthetic construct

Host Organism:

Homo sapiens

PDB Version:

Deposition Date:

2024-02-21

Release Date:

2025-01-15

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

5.20 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Spike glycoprotein
Mutations:F817P, A892P, A899P, A942P, K986P, V987P
Chain IDs:A, B, C
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)
Description:CeSPIACE
Chain IDs:D, E (auth: F), F (auth: H)
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