8YBM: Nanobody SEB-Nb6

Crystal structure of nanobody SEB-Nb6 bound to staphylococcal enterotoxin B (SEB). Determined by X-ray diffraction at 2.04 Å resolution. Released 25 Dec 2024.

Method: X-ray diffraction
Resolution: 2.04 Å
Organisms: Staphylococcus aureus, Vicugna pacos
Chains: 4
Atoms: 5,841
Mol. weight: 84.94 kDa
Released: 25 Dec 2024

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

Secondary structure: helices and β-sheets

8YBM contains 26 α-helices and 62 β-strands across 4 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: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	10-12	3
α-helix	16-18	3
β-strand	19	1	1
α-helix	24-27	4
α-helix	28-30	3
β-strand	35-40	6	2
β-strand	44	1	3
β-strand	50-54	5	3
β-strand	65-69	5	3
α-helix	73-79	7
β-strand	84-88	5	2
β-strand	91	1	3
β-strand	114-117	4	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	231-238	8	4

Chain B: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	6
β-strand	11-13	3	7
β-strand	19-26	8	6
β-strand	33	1	8
β-strand	36-41	6	7
β-strand	48-53	6	7
β-strand	59-61	3	7
α-helix	63-65	3
β-strand	69-74	6	6
β-strand	79-84	6	6
α-helix	89-91	3
β-strand	93-99	7	7
β-strand	103	1	8
β-strand	106-107	2	4
α-helix	114-116	3
β-strand	119-120	2	7
β-strand	124-128	5	7

Chain C: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	10-12	3
α-helix	16-18	3
β-strand	19	1	9
α-helix	24-27	4
α-helix	28-30	3
β-strand	35-40	6	10
β-strand	44	1	11
β-strand	50-56	7	11
β-strand	63-69	7	11
α-helix	73-79	7
β-strand	84-88	5	10
β-strand	91	1	11
β-strand	114-117	4	11
β-strand	120-122	3	10
β-strand	127-140	14	12
β-strand	143-154	12	12
β-strand	156-158	3	13
α-helix	159-174	16
β-strand	184-193	10	12
β-strand	196-201	6	12
α-helix	204-205	2
β-strand	207	1	9
α-helix	212-216	5
α-helix	217-221	5
β-strand	224-226	3	13
β-strand	231-238	8	12

Chain D: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	14
β-strand	11-13	3	15
β-strand	19-26	8	14
β-strand	33	1	16
β-strand	36-41	6	15
β-strand	48-53	6	15
β-strand	59-61	3	15
α-helix	63-65	3
β-strand	69-73	5	14
β-strand	80-84	5	14
α-helix	89-91	3
β-strand	93-99	7	15
β-strand	103	1	16
β-strand	106-107	2	12
α-helix	114-116	3
β-strand	119-120	2	15
β-strand	124-128	5	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Enterotoxin type B	A, C	protein	240	Staphylococcus aureus	P01552 (AlphaFold model)
nanobody SEB-Nb6	B, D	protein	129	Vicugna pacos

Sequence of entity 1 (A, C), FASTA

>8YBM_1 Enterotoxin type B (chains A, C)
MESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLG
NYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVT
EHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNN
SPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK

Sequence of entity 2 (B, D), FASTA

>8YBM_2 nanobody SEB-Nb6 (chains B, D)
QVQLVESGGGSVQAGGSLRLSCGPSGYSDDSRFSMGWFRQAPGKEREGVAVINSHGDTAY
ADSVKGRFTISKDNGRNTLILQMNSLKPEDTAIYVCASTRAYQLYSGSRSLRPVDYDYWG
QGTQVTVSS

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…
8YKT 2.04 Å, Fab and SEB complex
8YBP 2.08 Å, Crystal structure of nanobody SEB-Nb20 bound to staphylococcal enterotoxin B (SEB)
8YBN 2.18 Å, Crystal structure of nanobody SEB-Nb8 bound to staphylococcal enterotoxin B (SEB)
1SE3 2.3 Å, Staphylococcal enterotoxin B complexed with GM3 trisaccharide

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