2NX5: ELS4 TCR

Crystal structure of ELS4 TCR bound to HLA-B*3501 presenting EBV peptide EPLPQGQLTAY at 1.7A. Determined by X-ray diffraction at 2.7 Å resolution. Released 27 Feb 2007.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 20
Atoms: 26,481
Mol. weight: 372.98 kDa
Released: 27 Feb 2007

Explore 2NX5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2NX5 contains 98 α-helices and 286 β-strands across 19 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	1
β-strand	18-28	11	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
α-helix	182	1
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chains C, M and S: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Chain D: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	8
β-strand	9-13	5	9
β-strand	18-24	7	8
β-strand	29-37	9	9
β-strand	43-49	7	9
β-strand	53-57	5	8
β-strand	62-67	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-94	9	9
β-strand	105-106	2	9
β-strand	110-115	6	9
α-helix	116	1
β-strand	124-128	5	10
β-strand	129-130	2	11
β-strand	138-142	5	10
β-strand	158-160	3	10
α-helix	161-163	3
β-strand	164-168	5	10
β-strand	173-182	10	10

Chain E: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	13
β-strand	19-24	6	12
β-strand	31-37	7	13
β-strand	43-51	9	13
β-strand	54-57	4	13
β-strand	66-68	3	12
β-strand	74-79	6	12
α-helix	84-86	3
β-strand	88-95	8	13
β-strand	107-108	2	13
β-strand	112-117	6	13
α-helix	120-122	3
β-strand	124	1	14
α-helix	125-126	2
β-strand	127-132	6	11
α-helix	133-134	2
α-helix	135-141	7
β-strand	143-153	11	11
β-strand	154	1	14
β-strand	158-164	7	15
β-strand	167-169	3	15
β-strand	173-175	3	11
β-strand	180-181	2	11
β-strand	191-200	10	11
α-helix	201-204	4
β-strand	210-217	8	15
β-strand	220	1	16
α-helix	231-232	2
β-strand	234	1	16
β-strand	236-243	8	15

Chain F: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	17
α-helix	20	1
β-strand	21-28	8	17
β-strand	31-37	7	17
β-strand	46-47	2	17
α-helix	57-84	28
β-strand	93-103	11	17
β-strand	109-118	10	17
β-strand	121-126	6	17
β-strand	133-135	3	17
α-helix	139-149	11
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	18
α-helix	184-185	2
β-strand	186-193	8	19
β-strand	198-208	11	19
β-strand	209	1	18
β-strand	214-219	6	20
β-strand	222-223	2	20
β-strand	229-230	2	19
α-helix	231-233	3
β-strand	234-235	2	19
β-strand	241-250	10	19
α-helix	254-256	3
β-strand	257-262	6	20
β-strand	270-272	3	20

Chain G: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	21
α-helix	4-5	2
β-strand	6-11	6	22
β-strand	21-30	10	22
β-strand	31	1	21
β-strand	36-41	6	23
β-strand	44-45	2	23
α-helix	46	1
β-strand	50-51	2	22
α-helix	52-54	3
β-strand	55-56	2	22
β-strand	62-70	9	22
β-strand	78-83	6	23
α-helix	90	1
β-strand	91-94	4	23

Chain I: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	24
β-strand	9-13	5	25
β-strand	17-24	8	24
β-strand	29-37	9	25
α-helix	42-43	2
β-strand	44-49	6	25
β-strand	53-57	5	24
β-strand	62-67	6	24
α-helix	68-70	3
β-strand	72-78	7	24
α-helix	82-84	3
β-strand	86-94	9	25
β-strand	105-106	2	25
β-strand	110-115	6	25
β-strand	124-129	6	26
β-strand	130	1	27
β-strand	137-142	6	26
α-helix	151-153	3
β-strand	159-160	2	26
α-helix	161-163	3
β-strand	164-168	5	26
β-strand	173-181	9	26

9 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA-B35	A, F, K, Q	protein	276	Homo sapiens	P01889 (AlphaFold model)
Beta-2-microglobulin	B, G, L, R	protein	99	Homo sapiens	P61769 (AlphaFold model)
EBV peptide, EPLPQGQLTAY	C, H, M, S	protein	11		P03206 (AlphaFold model)
ELS4 TCR alpha chain	D, I, N, T	protein	188	Homo sapiens	P01848 (AlphaFold model)
ELS4 TCR beta chain	E, J, P, U	protein	243	Homo sapiens	P01850

Sequence of entity 1 (A, F, K, Q), FASTA

>2NX5_1 HLA-B35 (chains A, F, K, Q)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, G, L, R), FASTA

>2NX5_2 Beta-2-microglobulin (chains B, G, L, R)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H, M, S), FASTA

>2NX5_3 EBV peptide, EPLPQGQLTAY (chains C, H, M, S)
EPLPQGQLTAY

Sequence of entity 4 (D, I, N, T), FASTA

>2NX5_4 ELS4 TCR alpha chain (chains D, I, N, T)
QNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRFS
SFLSRSKGYSYLLLKELQMKDSASYLCAVQASGGSYIPTFGRGTSLIVHPYIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFN

Sequence of entity 5 (E, J, P, U), FASTA

>2NX5_5 ELS4 TCR beta chain (chains E, J, P, U)
DAGITQSPRHKVTETGTPVTLRCHQTENHRYMYWYRQDPGHGLRLIHYSYGVKDTDKGEV
SDGYSVSRSKTEDFLLTLESATSSQTSVYFCATGTGDSNQPQHFGDGTRLSILEDLNKVF
PPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Primary citation

A T cell receptor flattens a bulged antigenic peptide presented by a major histocompatibility complex class I molecule. Tynan, F.E., Reid, H.H., Kjer-Nielsen, L. et al. Nat Immunol (2007) 8:268-276. DOI 10.1038/ni1432 · PubMed

Other PDB entries of the same protein (UniProt P01889 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1K5N 1.09 Å, HLA-B*2709 bound to nona-peptide M9
4U1M 1.18 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
6MT3 1.21 Å, Crystal Structure of HLA-B*18:01 in complex with NP338 influenza peptide
3LN4 1.3 Å, Crystal structure of HLA-B*4103 in complex with a 16mer self-peptide derived from…
3BWA 1.3 Å, Crystal Structure of HLA B*3508 in complex with a HCMV 8-mer peptide from the pp65 protein
3SPV 1.3 Å, Crystal structure of a peptide-HLA complex
6MT6 1.31 Å, Crystal Structure of HLA-B*37:01 in complex with NP338 influenza peptide
2BVP 1.35 Å, Structures of Three HIV-1 HLA-B5703-Peptide Complexes and Identification of Related HLAs…
6MTL 1.35 Å, Crystal Structure of HLA-B*44:05 in complex with NP338 influenza peptide
4U1J 1.38 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
6PYW 1.38 Å, Crystal Structure of HLA-B*2705-W60A in complex with LRN, a self-peptide

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