4UDU: Staphylococcal enterotoxin E

Crystal structure of staphylococcal enterotoxin E in complex with a T cell receptor. Determined by X-ray diffraction at 2.5 Å resolution. Released 24 Jun 2015.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: HOMO SAPIENS, STAPHYLOCOCCUS AUREUS
Chains: 3
Atoms: 4,915
Mol. weight: 77.5 kDa
Ligands: ZN
Released: 24 Jun 2015

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

Secondary structure: helices and β-sheets

4UDU contains 21 α-helices and 56 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 A: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	1
β-strand	11-14	4	2
β-strand	20-26	7	1
β-strand	33-38	6	2
β-strand	44-49	6	2
β-strand	53-57	5	1
β-strand	60-65	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-91	8	2
β-strand	100-102	3	2
β-strand	106-110	5	2
β-strand	120-126	7	3
β-strand	133-138	6	3
α-helix	144-147	4
β-strand	154-156	3	3
α-helix	157-159	3
β-strand	160-164	5	3
β-strand	169-178	10	3

Chain B: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	4
β-strand	11-15	5	5
β-strand	20-25	6	4
β-strand	32-38	7	5
α-helix	43-44	2
β-strand	45-51	7	5
β-strand	54-58	5	5
β-strand	66-69	4	4
β-strand	76-80	5	4
α-helix	85-87	3
β-strand	90-96	7	5
β-strand	103-104	2	5
β-strand	108-113	6	5
α-helix	116-118	3
β-strand	120	1	6
β-strand	123-128	6	3
α-helix	129-130	2
α-helix	131-137	7
β-strand	139-149	11	3
β-strand	150	1	6
β-strand	154-160	7	7
β-strand	163-165	3	7
β-strand	169-171	3	3
α-helix	175	1
β-strand	176-177	2	3
α-helix	185-186	2
β-strand	187-196	10	3
α-helix	197-201	5
β-strand	206-213	8	7
β-strand	216	1	8
α-helix	227-228	2
β-strand	230	1	8
β-strand	232-239	8	7

Chain C: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	15-17	3
α-helix	22-27	6
α-helix	28-32	5
β-strand	35-41	7	9
β-strand	51-54	4	10
β-strand	66-70	5	10
α-helix	74-78	5
β-strand	85-90	6	9
β-strand	91-92	2	10
β-strand	104-108	5	10
β-strand	111-113	3	9
β-strand	118-124	7	11
β-strand	127-131	5	12
β-strand	134-136	3	12
β-strand	144-147	4	11
β-strand	149-151	3	13
α-helix	152-167	16
α-helix	173-175	3
β-strand	181-187	7	12
β-strand	193-197	5	12
α-helix	206-209	4
α-helix	210-213	4
β-strand	218-220	3	13
β-strand	225-231	7	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T cell receptor alpha chain, T-cell receptor alpha chain C region	A	protein	206	HOMO SAPIENS	A0A0B4J277 (AlphaFold model), P01848 (AlphaFold model)
Protein TRBV7-9, T-cell receptor beta-2 chain C region	B	protein	243	HOMO SAPIENS	A0A5A3 (AlphaFold model), A0A5B9 (AlphaFold model)
Enterotoxin type E	C	protein	233	STAPHYLOCOCCUS AUREUS	P12993

Sequence of entity 1 (A), FASTA

>4UDU_1 T CELL RECEPTOR ALPHA CHAIN, T-CELL RECEPTOR ALPHA CHAIN C REGION (chains A)
MGIQVEQSPPDLILQEGANSTLRCNFSDSVNNLQWFHQNPWGQLINLFYIPSGTKQNGRL
SATTVATERYSLLYISSSQTTDSGVYFCAVDSATSGTYKYIFGTGTRLKVLANIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (B), FASTA

>4UDU_2 PROTEIN TRBV7-9, T-CELL RECEPTOR BETA-2 CHAIN C REGION (chains B)
MDTGVSQNPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSR
LLSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSLGGYEQYFGPGTRLTVTEDLKNVF
PPEVAVFVPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Sequence of entity 3 (C), FASTA

>4UDU_3 ENTEROTOXIN TYPE E (chains C)
SEKSEEINEKDLRKKSELQRNALSNLRQIYYYNEKAITENKESDDQFLENTLLFKGFFTG
HPWYNDLLVDLGSKDATNKYKGKKVDLYGAYYGYQCAGGTPNKTACMYGGVTLHDNNRLT
EEKKVPINLWIDGKQTTVPIDKVKTSKKEVTVQELDLQARHYLHGKFGLYNSDSFGGKVQ
RGLIVFHSSEGSTVSYDLFDAQGQYPDTLLRIYRDNKTINSENLHIDLYLYTT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Structure of Staphylococcal Enterotoxin E in Complex with Tcr Defines the Role of Tcr Loop Positioning in Superantigen Recognition. Rodstrom, K.E.J., Regenthal, P., Lindkvist-Petersson, K. PLoS One (2015) 10:01319. DOI 10.1371/JOURNAL.PONE.0131988 · PubMed

Other PDB entries of the same protein (UniProt A0A0B4J277 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4UDT 1.35 Å, T cell receptor (TRAV22,TRBV7-9) structure
6R2L 2.3 Å, NYBR1-A2-slskildtv
5FKA 2.4 Å, Crystal structure of staphylococcal enterotoxin E in complex with a T cell receptor
5MEN 2.81 Å, Human Leukocyte Antigen A02 presenting ILAKFLHWL, in complex with cognate T-Cell Receptor
5FK9 3.1 Å, Crystal structure of staphylococcal enterotoxin A F47A mutant in complex with a T cell…

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