5E6I: TCR PF8

Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2. Determined by X-ray diffraction at 4.0 Å resolution. Released 19 Oct 2016.

Method: X-ray diffraction
Resolution: 4.0 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 20
Atoms: 24,882
Mol. weight: 381.26 kDa
Released: 19 Oct 2016

Explore 5E6I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E6I contains 69 α-helices and 288 β-strands across 16 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: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	20
β-strand	10-14	5	21
β-strand	19-24	6	20
β-strand	32-37	6	21
β-strand	44-49	6	21
β-strand	53-56	4	20
β-strand	61-65	5	20
β-strand	71-76	6	20
β-strand	85-93	9	21
β-strand	100-103	4	21
β-strand	108-112	5	21
β-strand	121-127	7	22
β-strand	133-139	7	22
α-helix	146-150	5
β-strand	156-158	3	22
β-strand	162-164	3	23
β-strand	171-173	3	23
β-strand	176-178	3	22
α-helix	190-192	3

Chain B: 4 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	4	1
β-strand	5-6	2	24
β-strand	10-14	5	25
β-strand	19-21	3	26
β-strand	23-24	2	24
β-strand	31-37	7	25
β-strand	38	1	27
β-strand	42	1	27
β-strand	45-50	6	25
β-strand	54-57	4	25
β-strand	65-66	2	26
β-strand	73	1	24
β-strand	76-78	3	26
β-strand	88-94	7	25
β-strand	102	1	25
β-strand	107-112	6	25
α-helix	115-117	3
β-strand	119	1	28
β-strand	122	1	29
β-strand	125-127	3	22
α-helix	130-136	7
β-strand	140-141	2	30
β-strand	142-143	2	22
β-strand	146	1	29
β-strand	149	1	28
β-strand	153-159	7	31
β-strand	162-164	3	31
β-strand	168	1	30
β-strand	175-176	2	32
β-strand	186-187	2	32
β-strand	192-193	2	30
α-helix	196-200	5
β-strand	205-212	8	31
β-strand	215	1	33
β-strand	229	1	33
β-strand	232-238	7	31

Chain C: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	34
α-helix	19-20	2
β-strand	21-28	8	34
β-strand	32	1	34
β-strand	36	1	34
α-helix	51-54	4
α-helix	57-65	9
α-helix	68-84	17
β-strand	94-103	10	34
β-strand	109-118	10	34
β-strand	121-126	6	34
α-helix	128-130	3
β-strand	133-135	3	34
α-helix	138-150	13
α-helix	153-158	6
α-helix	159-163	5
α-helix	164-172	9
α-helix	176-179	4
β-strand	187-189	3	35
β-strand	192	1	36
β-strand	200	1	36
β-strand	201-208	8	35
β-strand	228	1	35
β-strand	234-235	2	35
β-strand	241-247	7	35
β-strand	260	1	37
β-strand	271	1	37

Chain D: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	38
β-strand	21-30	10	38
β-strand	36-41	6	39
β-strand	44-45	2	39
β-strand	50-51	2	38
α-helix	52-54	3
β-strand	55	1	38
β-strand	62-70	9	38
β-strand	78-83	6	39
β-strand	91	1	39

Chain F: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	40
β-strand	5-7	3	41
β-strand	10-14	5	42
β-strand	19-24	6	41
β-strand	32-37	6	42
α-helix	42-43	2
β-strand	45-49	5	42
β-strand	54-57	4	41
β-strand	61-64	4	41
β-strand	71-76	6	41
α-helix	81-83	3
β-strand	85-90	6	42
β-strand	103	1	42
β-strand	104	1	40
β-strand	107-112	6	42
β-strand	121-124	4	43
β-strand	126-127	2	44
β-strand	136-139	4	43
β-strand	156-157	2	43
β-strand	161-165	5	43
α-helix	166-168	3
β-strand	170-178	9	43
α-helix	186-189	4
β-strand	199	1	43

Chain G: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	32-37	6	2
β-strand	44-49	6	2
β-strand	53-55	3	1
β-strand	61-65	5	1
β-strand	72-76	5	1
α-helix	81-83	3
β-strand	85-91	7	2
β-strand	102-103	2	2
β-strand	107-112	6	2
α-helix	113-114	2
β-strand	121-127	7	3
β-strand	134-139	6	3
β-strand	156-157	2	3
β-strand	162-165	4	4
β-strand	170-173	4	4
β-strand	174-175	2	3
β-strand	177-179	3	3
α-helix	186-188	3

Chain H: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	5
β-strand	10-14	5	6
β-strand	19-23	5	5
β-strand	31-37	7	7
β-strand	44-49	6	7
β-strand	56	1	7
β-strand	65-66	2	5
β-strand	74-78	5	5
α-helix	83-85	3
β-strand	88-94	7	7
β-strand	107	1	7
β-strand	108-112	5	6
α-helix	115-117	3
β-strand	125-127	3	3
α-helix	128-129	2
α-helix	130-135	6
β-strand	139-141	3	8
β-strand	142-143	2	3
β-strand	144-148	5	9
β-strand	153-155	3	10
β-strand	158-159	2	10
β-strand	162-163	2	10
β-strand	168-170	3	8
β-strand	186-189	4	9
β-strand	190-194	5	8
α-helix	196-200	5
β-strand	206-212	7	10
α-helix	226-227	2
β-strand	231-236	6	10

Chain I: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	11
β-strand	21-28	8	11
β-strand	32	1	11
α-helix	57-85	29
β-strand	94-103	10	11
β-strand	109-118	10	11
β-strand	121-126	6	11
β-strand	133-135	3	11
α-helix	139-148	10
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-173	9
α-helix	176-179	4
β-strand	183	1	12
α-helix	184-185	2
β-strand	186-189	4	13
β-strand	192	1	14
β-strand	200-201	2	14
β-strand	203-206	4	13
β-strand	209	1	12
β-strand	214-216	3	15
β-strand	228-230	3	14
β-strand	234-235	2	13
β-strand	241-243	3	13
β-strand	245-248	4	14
β-strand	260-262	3	15
β-strand	270-271	2	15

8 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
TCR alpha chain,Human nkt tcr alpha chain	A, F, G, P	protein	208	Homo sapiens	K7N5M3 (AlphaFold model)
T-cell receptor beta-2 chain C region	B, H, L, Q	protein	243	Homo sapiens	A0A087WZ08
HLA class I histocompatibility antigen, A-2 alpha chain	C, I, M, R	protein	276	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	D, J, N, U	protein	100	Homo sapiens	P61769 (AlphaFold model)
Matrix protein 1	E, K, O, T	protein	9	Influenza A virus	P03485

Sequence of entity 1 (A, F, G, P), FASTA

>5E6I_1 TCR alpha chain,Human nkt tcr alpha chain (chains A, F, G, P)
MGQQLNQSPQSMFIQEGEDVSMNCTSSSIFNTWLWYKQEPGEGPVLLIALYKAGELTSNG
RLTAQFGITRKDSFLNISASIPSDVGIYFCAGPGGSSNTGKLIFGQGTTLQVKPDIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (B, H, L, Q), FASTA

>5E6I_2 T-cell receptor beta-2 chain C region (chains B, H, L, Q)
MEAQVTQNPRYLITVTGKELTVTCSQNMNHEYMSWYRQDPGLGLRQIYYSMNVEVTDKGD
VPEGYKVSRKEKRNFPLILESPSPNQTSLYFCASSLIYPGELFFGEGSRLTVLEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Sequence of entity 3 (C, I, M, R), FASTA

>5E6I_3 HLA class I histocompatibility antigen, A-2 alpha chain (chains C, I, M, R)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 4 (D, J, N, U), FASTA

>5E6I_4 Beta-2-microglobulin (chains D, J, N, U)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 5 (E, K, O, T), FASTA

>5E6I_5 Matrix protein 1 (chains E, K, O, T)
GILGFVFTL

Primary citation

Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2. Gao, M. To be published.

Other PDB entries of the same protein (UniProt K7N5M3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MJJ 1.93 Å, Crystal structure of the mCD1d/xxm (JJ290) /iNKTCR ternary complex
6MJ4 2.0 Å, Crystal structure of MCD1D/INKTCR TERNARY COMPLEX bound to glycolipid (XXW)
6MIV 2.05 Å, Crystal structure of the mCD1d/xxq (JJ300)/iNKTCR ternary complex
5WLG 2.1 Å, Crystal Structure of H-2Db with the GAP501 peptide (SQL)
6MJI 2.3 Å, Crystal structure of the mCD1d/xxs (JJ304) /iNKTCR ternary complex
6R2L 2.3 Å, NYBR1-A2-slskildtv
6D78 2.35 Å, The complex between high-affinity TCR DMF5(alpha-D26Y,beta-L98W) and human Class I MHC…
6MJA 2.35 Å, Crystal structure of the mCD1d/xxo (JJ294) /iNKTCR ternary complex
6MJ6 2.45 Å, Crystal structure of the mCD1d/xxx (JJ166) /iNKTCR ternary complex
4EN3 2.57 Å, Crystal structure of a human Valpha24(-) NKT TCR in complex with…
8T4Z 2.69 Å, T-cell receptor and lipid complex structure
6MIY 2.75 Å, Crystal structure of the mCD1d/xxa (JJ239)/iNKTCR ternary complex

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