4RGO: Staphylococcal Enterotoxin B

Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 14G8. Determined by X-ray diffraction at 1.8 Å resolution. Released 21 Jan 2015.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Staphylococcus aureus, Mus musculus
Chains: 3
Atoms: 6,100
Mol. weight: 76.41 kDa
Released: 21 Jan 2015

Explore 4RGO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4RGO contains 26 α-helices and 62 β-strands across 3 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 H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	45-51	7	9
β-strand	57-58	2	9
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	87-89	3
β-strand	91-97	7	9
β-strand	103	1	5
β-strand	109-110	2	9
β-strand	114-116	3	9
β-strand	117-118	2	8
α-helix	121-123	3
β-strand	124	1	10
α-helix	125-126	2
β-strand	127-131	5	11
β-strand	142-152	11	11
β-strand	153	1	10
β-strand	158-161	4	12
α-helix	162-164	3
β-strand	170-172	3	11
α-helix	173-175	3
β-strand	176-178	3	11
β-strand	181-191	11	11
α-helix	192-194	3
β-strand	201-206	6	12
α-helix	207-209	3
β-strand	211-216	6	12

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	13
β-strand	10-13	4	14
β-strand	18-25	8	13
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
β-strand	62-66	5	13
β-strand	70-76	7	13
α-helix	80-82	3
β-strand	84-90	7	14
α-helix	96	1
β-strand	97-98	2	14
β-strand	102-106	5	14
β-strand	111	1	15
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	145-150	6	17
β-strand	153	1	17
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-187	5
β-strand	191-197	7	17
α-helix	204	1
β-strand	205-210	6	17

Chain S: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
α-helix	12-13	2
α-helix	14-16	3
β-strand	17	1	1
α-helix	22-25	4
α-helix	26-28	3
β-strand	33-38	6	2
β-strand	42	1	3
β-strand	48-51	4	3
β-strand	63-67	5	3
α-helix	71-77	7
β-strand	82-86	5	2
β-strand	89	1	3
β-strand	111-115	5	3
β-strand	118-120	3	2
β-strand	125-138	14	4
β-strand	140	1	5
β-strand	141-152	12	4
β-strand	154-156	3	6
α-helix	157-172	16
β-strand	182-191	10	4
β-strand	194-199	6	4
α-helix	202-203	2
β-strand	205	1	1
α-helix	210-214	5
α-helix	215-217	3
β-strand	222-224	3	6
β-strand	229-236	8	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Enterotoxin type B	S	protein	245	Staphylococcus aureus	P01552 (AlphaFold model)
14G8 heavy chain	H	protein	222	Mus musculus
14G8 light chain	L	protein	214	Mus musculus

Sequence of entity 1 (S), FASTA

>4RGO_1 Enterotoxin type B (chains S)
GSEFGSESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIK
DTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCM
YGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKL
YEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYL
TTKKK

Sequence of entity 2 (H), FASTA

>4RGO_2 14G8 heavy chain (chains H)
EVNLIESGGDLVKPGGSLKLSCATSGFTFSAYGLSWVRQTPERRLEWVASISGGGSVYYP
DSVKGRFTISRDTAGDILFLQMNSLRSEDSAIYYCVRDLYGDYVGRYAYWGQGTLVIVSA
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 3 (L), FASTA

>4RGO_3 14G8 light chain (chains L)
DIVMTQSPATLSVTPGDRVSLSCRASQSIGDYLHWYQQKSHESPRLLINYASQSISGIPS
RFSGSGSGSDFTLIINSVEPEDVGVYYCQNGHSFPYTFGGGTKLEIRRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Mechanisms mediating enhanced neutralization efficacy of staphylococcal enterotoxin B by combinations of monoclonal antibodies. Dutta, K., Varshney, A.K., Franklin, M.C. et al. J Biol Chem (2015) 290:6715-6730. DOI 10.1074/jbc.M114.630715 · 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)
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)
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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