4RGM: Staphylococcal Enterotoxin B

Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 20B1. Determined by X-ray diffraction at 2.69 Å resolution. Released 21 Jan 2015.

Method: X-ray diffraction
Resolution: 2.69 Å
Organisms: Staphylococcus aureus, Mus musculus
Chains: 6
Atoms: 10,526
Mol. weight: 153.84 kDa
Released: 21 Jan 2015

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

Secondary structure: helices and β-sheets

4RGM contains 50 α-helices and 120 β-strands across 6 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	3-7	5
α-helix	12-13	2
α-helix	14-16	3
β-strand	17	1	16
α-helix	22-25	4
α-helix	26-28	3
β-strand	33-38	6	17
β-strand	42	1	18
β-strand	48-51	4	18
β-strand	63-67	5	18
α-helix	71-77	7
β-strand	82-86	5	17
β-strand	89	1	18
β-strand	111-115	5	18
β-strand	118-120	3	17
β-strand	125-138	14	19
β-strand	141-152	12	19
β-strand	154-156	3	20
α-helix	157-172	16
β-strand	182-191	10	19
β-strand	194-199	6	19
α-helix	202-203	2
β-strand	205	1	16
α-helix	210-214	5
α-helix	215-219	5
β-strand	222-224	3	20
β-strand	229-236	8	19

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10-13	4	22
β-strand	19-25	7	21
β-strand	33-38	6	22
β-strand	44-49	6	22
β-strand	53-54	2	22
α-helix	55	1
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	85-90	6	22
α-helix	96	1
β-strand	97-98	2	22
β-strand	102-106	5	22
β-strand	111	1	23
β-strand	114-118	5	24
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	24
β-strand	140	1	23
β-strand	145-150	6	25
β-strand	153-155	3	25
β-strand	159-163	5	24
α-helix	164-167	4
β-strand	173-182	10	24
α-helix	183-186	4
β-strand	191-197	7	25
β-strand	205-210	6	25

Chain C: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	26
α-helix	7-9	3
β-strand	10-12	3	27
β-strand	18-25	8	26
α-helix	29-31	3
β-strand	33-39	7	27
β-strand	45-51	7	27
β-strand	58-60	3	27
β-strand	68-73	6	26
α-helix	74-76	3
β-strand	78-83	6	26
α-helix	88-90	3
β-strand	92-99	8	27
β-strand	111	1	27
β-strand	115-119	5	27
β-strand	125	1	28
α-helix	126-127	2
β-strand	128-132	5	29
β-strand	143-153	11	29
β-strand	154	1	28
β-strand	159-162	4	30
α-helix	163-165	3
β-strand	167	1	30
β-strand	171-173	3	29
α-helix	174-176	3
β-strand	177-179	3	29
β-strand	182-192	11	29
β-strand	202-207	6	30
α-helix	208-210	3
β-strand	212-217	6	30

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	107-111	5	12
β-strand	115-119	5	12
β-strand	125	1	13
α-helix	126-127	2
β-strand	128-132	5	14
β-strand	143-153	11	14
β-strand	154	1	13
β-strand	159-162	4	15
α-helix	163-165	3
β-strand	167	1	15
β-strand	171-173	3	14
α-helix	174-176	3
β-strand	177-179	3	14
β-strand	182-192	11	14
β-strand	202-207	6	15
α-helix	208-210	3
β-strand	212-217	6	15

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	33-38	6	7
β-strand	44-49	6	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-66	5	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	8
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	145-150	6	10
β-strand	153-155	3	10
β-strand	159-163	5	9
β-strand	173-182	10	9
α-helix	183-186	4
β-strand	191-197	7	10
α-helix	204	1
β-strand	205-210	6	10

Chain S: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
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	48-52	5	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	141-152	12	4
β-strand	154-156	3	5
α-helix	157-171	15
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	215-219	5
β-strand	222-224	3	5
β-strand	228-236	9	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Enterotoxin type B	A, S	protein	245	Staphylococcus aureus	P01552 (AlphaFold model)
20B1 light chain	B, L	protein	214	Mus musculus
20B1 heavy chain	C, H	protein	223	Mus musculus

Sequence of entity 1 (A, S), FASTA

>4RGM_1 Enterotoxin type B (chains A, S)
GSEFGSESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIK
DTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCM
YGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKL
YEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYL
TTKKK

Sequence of entity 2 (B, L), FASTA

>4RGM_2 20B1 light chain (chains B, L)
DIQMTQSPSSLSASLGERVSLTCRASQEISDYLTWLQQKPDGTIKRLIYVASSLDSGVPK
RFSGSRSGSDYSLTISSLESEDFADYYCLQYANYPWTFGGGTKLEIRRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (C, H), FASTA

>4RGM_3 20B1 heavy chain (chains C, H)
QIQLVQSGPELKKPGETVRISCKASGYIFTIAGIQWVQKMPGRGLRWIGWINTHSGVPEY
AEEFKGRFAFSLETSARTAYLQISNLKDEDTATYFCARIYYGNNGGVMDYWGQGTSVTVS
SAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQS
DLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

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)
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)
8YBN 2.18 Å, Crystal structure of nanobody SEB-Nb8 bound to staphylococcal enterotoxin B (SEB)

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