2XN9: T cell receptor alpha chain C region

Crystal structure of the ternary complex between human T cell receptor, staphylococcal enterotoxin H and human major histocompatibility complex class II. Determined by X-ray diffraction at 2.3 Å resolution. Released 24 Nov 2010.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: HOMO SAPIENS, STAPHYLOCOCCUS AUREUS, INFLUENZA A VIRUS
Chains: 6
Atoms: 8,711
Mol. weight: 120.41 kDa
Released: 24 Nov 2010

Explore 2XN9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XN9 contains 38 α-helices and 91 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: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	10-14	5	2
β-strand	19-24	6	1
β-strand	32-37	6	2
β-strand	44-49	6	2
β-strand	55-58	4	1
β-strand	61-65	5	1
β-strand	71-76	6	1
α-helix	81-83	3
β-strand	85-91	7	2
β-strand	99-100	2	2
β-strand	104-109	6	2
α-helix	110-111	2
β-strand	118-124	7	3
β-strand	131-136	6	3
α-helix	145-147	3
β-strand	152-154	3	3
α-helix	155-157	3
β-strand	158-162	5	3
α-helix	163-165	3
β-strand	167-176	10	3
α-helix	183-186	4
β-strand	197	1	3

Chain B: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	4
β-strand	12-16	5	5
β-strand	21-23	3	6
β-strand	24-27	4	4
β-strand	33-40	8	5
β-strand	44-51	8	5
β-strand	58-59	2	5
β-strand	66-68	3	6
β-strand	75	1	4
β-strand	78-80	3	6
β-strand	89-96	8	5
α-helix	102-103	2
β-strand	104-105	2	5
β-strand	109-114	6	5
α-helix	117-119	3
β-strand	121	1	7
α-helix	122-123	2
β-strand	124-129	6	3
α-helix	130-131	2
α-helix	132-138	7
β-strand	140-150	11	3
β-strand	151	1	7
β-strand	155-161	7	8
β-strand	164-166	3	8
β-strand	170-172	3	3
α-helix	176	1
β-strand	177-178	2	3
β-strand	188-197	10	3
α-helix	198-201	4
β-strand	207-214	8	8
β-strand	217	1	9
α-helix	228-229	2
β-strand	231	1	9
β-strand	233-240	8	8

Chain C: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	6-8	3
α-helix	11-22	12
β-strand	25-30	6	10
β-strand	35-36	2	11
β-strand	40-43	4	11
α-helix	48-50	3
β-strand	52-56	5	11
α-helix	60-66	7
β-strand	71-75	5	10
β-strand	77-78	2	11
α-helix	82-84	3
β-strand	90-94	5	11
β-strand	97-99	3	10
β-strand	103-116	14	12
β-strand	119-120	2	12
β-strand	124-130	7	12
β-strand	132-134	3	13
α-helix	135-150	16
β-strand	161-168	8	12
β-strand	174-177	4	12
α-helix	186-189	4
α-helix	190-193	4
β-strand	198-200	3	13
β-strand	204-212	9	12

Chain D: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	14
β-strand	19-27	9	14
β-strand	29-35	7	14
β-strand	40-43	4	14
α-helix	48-51	4
β-strand	53	1	15
α-helix	56-76	21
α-helix	80-84	5
β-strand	85	1	16
α-helix	86-87	2
β-strand	88-93	6	17
β-strand	103-112	10	17
β-strand	113	1	16
β-strand	118-123	6	18
β-strand	126-128	3	18
β-strand	133-134	2	17
β-strand	138-139	2	17
β-strand	145-153	9	17
β-strand	160-166	7	18
β-strand	174-179	6	18

Chain E: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	7-18	12	14
β-strand	23-32	10	14
β-strand	35-41	7	14
β-strand	47-49	3	14
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-85	5
α-helix	87-91	5
β-strand	95	1	19
α-helix	96-97	2
β-strand	98-103	6	20
β-strand	113-122	10	20
β-strand	123	1	19
β-strand	128-133	6	21
β-strand	136-138	3	21
β-strand	142-144	3	20
β-strand	148-149	2	20
β-strand	155-163	9	20
β-strand	171-176	6	21
β-strand	184-188	5	21

Chain F: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	15
α-helix	6-8	3
α-helix	10-12	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T cell receptor alpha chain C region	A	protein	204	HOMO SAPIENS	P01848 (AlphaFold model)
T cell receptor beta-1 chain C region	B	protein	244	HOMO SAPIENS	P01850 (AlphaFold model)
Enterotoxin H	C	protein	217	STAPHYLOCOCCUS AUREUS	P0A0M0 (AlphaFold model)
HLA class II histocompatibility antigen, dr alpha chain,	D	protein	182	HOMO SAPIENS	P01903 (AlphaFold model)
Major histocompatibility complex class II beta chain	E	protein	190	HOMO SAPIENS	P01911
Hemagglutinin	F	protein	13	INFLUENZA A VIRUS	Q03909

Sequence of entity 1 (A), FASTA

>2XN9_1 T CELL RECEPTOR ALPHA CHAIN C REGION (chains A)
MQLLEQSPQFLSIQEGENLTVYCNSSSVFSSLQWYRQEPGEGPVLLVTVVTGGEVKKLKR
LTFQFGDARKDSSLHITAAQPGDTGLYLCAGAGSQGNLIFGKGTKLSVKPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (B), FASTA

>2XN9_2 T CELL RECEPTOR BETA-1 CHAIN C REGION (chains B)
MVDGGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKG
DIAEGYSVSREKKESFPLTVTSAQKNPTAFYLCASSSRSSYEQYFGPGTRLTVTEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Sequence of entity 3 (C), FASTA

>2XN9_3 ENTEROTOXIN H (chains C)
EDLHDKSELTDLALANAYGQYNHPFIKENIKSDEISGEKDLIFRNQGDSGNDLRVKFATA
DLAQKFKNKNVDIYGASFYYKCEKISENISECLYGGTTLNSEKLAQERVIGANVWVDGIQ
KETELIRTNKKNVTLQELDIKIRKILSDKYKIYYKDSEISKGLIEFDMKTPRDYSFDIYD
LKGENDYEIDKIYEDNKTLKSDDISHIDVNLYTKKKV

Sequence of entity 4 (D), FASTA

>2XN9_4 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN, (chains D)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DA

Sequence of entity 5 (E), FASTA

>2XN9_5 MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II BETA CHAIN (chains E)
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRA

Sequence of entity 6 (F), FASTA

>2XN9_6 HEMAGGLUTININ (chains F)
PKYVKQNTLKLAT

Primary citation

The Structure of Superantigen Complexed with Tcr and Mhc Reveals Novel Insights Into Superantigenic T Cell Activation. Saline, M., Rodstrom, K.E.J., Fischer, G. et al. Nat Commun (2010) 1:119. DOI 10.1038/NCOMMS1117 · PubMed

Other PDB entries of the same protein (UniProt P01848 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4UDT 1.35 Å, T cell receptor (TRAV22,TRBV7-9) structure
4WW1 1.38 Å, Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8 and Beta Chain-TRBV7-8
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
2BNU 1.4 Å, Structural and kinetic basis for heightened immunogenicity of T cell vaccines
1KGC 1.5 Å, Immune Receptor
2BNQ 1.7 Å, Structural and kinetic basis for heightened immunogenicity of T cell vaccines
2BNR 1.9 Å, Structural and kinetic basis for heightened immunogenicity of T cell vaccines
2IAL 1.92 Å, Structural basis for recognition of mutant self by a tumor-specific, MHC class…
5C0C 1.97 Å, 1E6 TCR in complex with HLA-A02 carrying RQFGPDWIVA
2VLM 1.98 Å, The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are…
5KSA 2.0 Å, Bel602-DQ8.5-glia-gamma1 complex
7RYL 2.0 Å, T cell receptor CO3

Browse structure collections

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