ISDA: 9NFU

Deposition Date 2025-02-21

Release Date 2025-11-12

Last Version Date 2025-11-12

Entry Detail

PDB ID:

9NFU

Keywords:

DE NOVO PROTEIN

Title:

CryoEM Structure of De Novo Antibody Fragment scFv 6 with C. difficile Toxin B (TcdB)

Biological Source:

Source Organism:

Clostridioides difficile (Taxon ID: 1496)
synthetic construct (Taxon ID: 32630)

Host Organism:

Priestia megaterium NBRC 15308 = ATCC 14581

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.60 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Toxin B
Gene (Uniprot):tcdB
Chain IDs:A
Chain Length:2119
Number of Molecules:1
Biological Source:Clostridioides difficile

UniProt ID:P18177 Pfam ID:PF12918, PF12919, PF11713, PF12920, PF01473, PF19127 EC:2.4.1.B62

Polymer Type:polypeptide(L)
Molecule:scFv 6 Heavy Chain, scFv 6 Light Chain
Chain IDs:B (auth: C)
Chain Length:278
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

Primary Citation

Atomically accurate de novo design of antibodies with RFdiffusion

Bennett, N.R, Watson, J.L, Ragotte, R.J, Borst, A.J, See, D.L, Weidle, C, Biswas, R, Yu, Y, Shrock, E.L, Ault, R, Leung, P.J.Y, Huang, B, Goreshnik, I, Tam, J, Carr, K.D, Singer, B, Criswell, C, Wicky, B.I.M, Vafeados, D, Sanchez, M.G, Kim, H.M, Torres, S.T, Chan, S, Sun, S.M, Spear, T, Sun, Y, O'Reilly, K, Maris, J.M, Sgourakis, N.G, Melnyk, R.A, Liu, C.C, Baker, D.Show

Nature ? ? ? (2025)

DOI: 10.1038/s41586-025-09721-5

Primary Citation of related structures

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