8YBN: Nanobody SEB-Nb8

Crystal structure of nanobody SEB-Nb8 bound to staphylococcal enterotoxin B (SEB). Determined by X-ray diffraction at 2.18 Å resolution. Released 25 Dec 2024.

Method: X-ray diffraction
Resolution: 2.18 Å
Organisms: Staphylococcus aureus, Vicugna pacos
Chains: 2
Atoms: 2,975
Mol. weight: 42.97 kDa
Released: 25 Dec 2024

Explore 8YBN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YBN contains 15 α-helices and 28 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	16-18	3
β-strand	19	1	1
α-helix	24-27	4
α-helix	28-30	3
β-strand	35-41	7	2
β-strand	44	1	3
β-strand	50-56	7	3
β-strand	63-69	7	3
α-helix	73-79	7
β-strand	83-88	6	2
β-strand	91	1	3
β-strand	113-117	5	3
β-strand	120-122	3	2
β-strand	127-140	14	4
β-strand	143-154	12	4
β-strand	156-158	3	5
α-helix	159-174	16
β-strand	184-193	10	4
β-strand	196-201	6	4
α-helix	204-205	2
β-strand	207	1	1
α-helix	212-216	5
α-helix	217-219	3
β-strand	224-226	3	5
β-strand	230-238	9	4

Chain B: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-13	4	7
β-strand	18-25	8	6
β-strand	33-39	7	7
β-strand	46-52	7	7
β-strand	57-60	4	7
α-helix	62-64	3
β-strand	68-73	6	6
α-helix	74-76	3
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-98	7	7
α-helix	99-100	2
α-helix	109-111	3
α-helix	115-117	3
β-strand	120-121	2	7
β-strand	125-130	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Enterotoxin type B	A	protein	240	Staphylococcus aureus	P01552 (AlphaFold model)
nanobody SEB-Nb8	B	protein	131	Vicugna pacos

Sequence of entity 1 (A), FASTA

>8YBN_1 Enterotoxin type B (chains A)
MESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLG
NYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVT
EHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNN
SPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK

Sequence of entity 2 (B), FASTA

>8YBN_2 nanobody SEB-Nb8 (chains B)
QVQLVESGGGSVQDGGSLRLSCAASGFTIDNRWMTWFRQAPGKEREGVASILTYSGRTVY
ADSGKGRFTISQANAKNSVYLQMNSLKPEDTATYYCAAGDAYHKWFMPSSRALDRKEYNY
WGQGTLVTVSS

Primary citation

Structural insights into the binding of nanobodies to the Staphylococcal enterotoxin B. Zong, X., Liu, P., Wang, Z. et al. Int J Biol Macromol (2024) 276:133957-133957. DOI 10.1016/j.ijbiomac.2024.133957 · PubMed

Other PDB entries of the same protein (UniProt P01552 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3SEB 1.48 Å, Staphylococcal enterotoxin B
8YBO 1.59 Å, Crystal structure of nanobody SEB-Nb11 bound to staphylococcal enterotoxin B (SEB)
4RGO 1.8 Å, Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 14G8
1SE4 1.9 Å, Staphylococcal enterotoxin B complexed with lactose
3GP7 1.9 Å, Staphylococcal Enterotoxin B mutant N23YK97SK98S
1D5M 2.0 Å, X-ray crystal structure of HLA-DR4 complexed with peptide and seb
1D5Z 2.0 Å, X-ray crystal structure of HLA-DR4 complexed with peptidomimetic and seb
1GOZ 2.0 Å, Structural basis for the altered T-cell receptor binding specificty in a superantigenic…
8YBM 2.04 Å, Crystal structure of nanobody SEB-Nb6 bound to staphylococcal enterotoxin B (SEB)
8YKT 2.04 Å, Fab and SEB complex
8YBP 2.08 Å, Crystal structure of nanobody SEB-Nb20 bound to staphylococcal enterotoxin B (SEB)
1SE3 2.3 Å, Staphylococcal enterotoxin B complexed with GM3 trisaccharide

Browse structure collections

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