4EUP: PDB entry 4EUP

The complex between TCR JKF6 and human Class I MHC HLA-A2 presenting the MART-1(27-35)(A27L) peptide. Determined by X-ray diffraction at 2.88 Å resolution. Released 1 May 2013.

Method: X-ray diffraction
Resolution: 2.88 Å
Organism: Homo sapiens
Chains: 10
Atoms: 13,167
Mol. weight: 189.68 kDa
Released: 1 May 2013

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

Secondary structure: helices and β-sheets

4EUP contains 47 α-helices and 145 β-strands across 10 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: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	9
α-helix	20	1
β-strand	21-28	8	9
β-strand	31-37	7	9
β-strand	46-47	2	9
α-helix	50-54	5
α-helix	57-85	29
β-strand	94-103	10	9
β-strand	109-118	10	9
β-strand	121-126	6	9
β-strand	133-135	3	9
α-helix	139-149	11
α-helix	152-160	9
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	10
α-helix	184-185	2
β-strand	186-193	8	11
β-strand	198-208	11	11
β-strand	209	1	10
β-strand	213-216	4	12
β-strand	228-230	3	11
β-strand	234-235	2	11
β-strand	241-250	10	11
α-helix	254-256	3
β-strand	259-263	5	12
β-strand	270-272	3	12

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	13
α-helix	4-5	2
β-strand	6-11	6	14
β-strand	21-30	10	14
β-strand	31	1	13
β-strand	36-41	6	15
β-strand	44-45	2	15
α-helix	46	1
β-strand	50-51	2	14
β-strand	55-56	2	14
β-strand	62-70	9	14
β-strand	78-83	6	15
β-strand	91-94	4	15

Chains C and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	16

Chain D: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	21-28	8	1
β-strand	31-37	7	1
α-helix	51-54	4
α-helix	57-85	29
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	140-149	10
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-194	9	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-217	4	4
β-strand	229-230	2	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	259-262	4	4
β-strand	270-272	3	4

Chain E: 2 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	35-41	7	7
β-strand	44-45	2	7
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	78-84	7	7
β-strand	91-94	4	7

Chain G: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	17
β-strand	12-15	4	18
β-strand	20-26	7	17
β-strand	34-39	6	18
β-strand	46-51	6	18
β-strand	55-59	5	17
β-strand	62-67	6	17
β-strand	72-77	6	17
α-helix	82-84	3
β-strand	86-93	8	18
β-strand	100-102	3	18
α-helix	103	1
β-strand	106-111	6	18
α-helix	112	1
β-strand	120-126	7	19
β-strand	133-138	6	19
α-helix	147-149	3
β-strand	154-156	3	19
α-helix	157-159	3
β-strand	160-164	5	19
β-strand	169-178	10	19
β-strand	199	1	19

Chain H: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	24
β-strand	10-14	5	25
β-strand	19-21	3	24
β-strand	23-25	3	24
β-strand	31-38	8	25
β-strand	42-49	8	25
β-strand	56-57	2	25
β-strand	64-70	7	24
β-strand	73-78	6	24
α-helix	83-85	3
β-strand	87-94	8	25
β-strand	97	1	8
β-strand	103-104	2	25
β-strand	108-113	6	25
α-helix	116-118	3
β-strand	120	1	26
α-helix	121-122	2
β-strand	123-128	6	19
α-helix	129-130	2
α-helix	131-137	7
β-strand	139-149	11	19
β-strand	150	1	26
β-strand	154-160	7	27
β-strand	163-165	3	27
β-strand	169-171	3	19
α-helix	175	1
β-strand	176-177	2	19
β-strand	187-196	10	19
α-helix	197-201	5
β-strand	206-213	8	27
β-strand	216	1	28
β-strand	230	1	28
β-strand	232-239	8	27

Chain I: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	20
α-helix	9	1
β-strand	10-13	4	21
β-strand	18-24	7	20
β-strand	32-37	6	21
β-strand	43-49	7	21
β-strand	53-57	5	20
β-strand	60-65	6	20
β-strand	70-75	6	20
α-helix	80-82	3
β-strand	84-90	7	21
β-strand	99-100	2	21
β-strand	104-109	6	21
α-helix	110	1
β-strand	118-123	6	22
β-strand	124	1	23
β-strand	131-136	6	22
β-strand	152-154	3	22
β-strand	158-162	5	22
α-helix	163-165	3
β-strand	167-176	10	22
β-strand	197	1	22

1 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 class I histocompatibility antigen, A-2 alpha chain	A, D	protein	275	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	100	Homo sapiens	P61769 (AlphaFold model)
Melanoma antigen recognized by T-cells 1	C, F	protein	9	Homo sapiens	Q16655 (AlphaFold model)
JKF6 alpha chain	G, I	protein	206	Homo sapiens
JKF6 beta chain	H, J	protein	243	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>4EUP_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A, D)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B, E), FASTA

>4EUP_2 Beta-2-microglobulin (chains B, E)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F), FASTA

>4EUP_3 Melanoma antigen recognized by T-cells 1 (chains C, F)
ALGIGILTV

Sequence of entity 4 (G, I), FASTA

>4EUP_4 JKF6 alpha chain (chains G, I)
MQKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMSIYSNGDKEDG
RFTAQLNKASQYVSLLIRDAQPSDSATYLCAVSGGGADGLTFGKGTQVVVTPNIQNPDPA
VYQLRDSKSADKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (H, J), FASTA

>4EUP_5 JKF6 beta chain (chains H, J)
MDKVTQSSRYLVKRTGEKVFLECVQDMDHENMFWYRQDPGLGLRLIYFSYDVKMKEKGDI
PEGYSVSREKKERFSLILASASTDQTSMYLCASSFLGTGVEQYFGPGTRLTVVEDLNKVF
PPEVALFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSEADEWTQDRAKPVTQIVSAEAWG
RAD

Primary citation

Structural description of how different MART-1 antigenic peptides influence JKF6 T cell receptor recognition. Hossain, M., Baker, B.M. To be published.

Other PDB entries of the same protein (UniProt P04439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
3D25 1.3 Å, Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC…
3MRG 1.3 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081…
6JOZ 1.35 Å, Crystal structure of BRLF peptide from EBV in complex with HLA-A1101.
5C0G 1.37 Å, HLA-A02 carrying YLGGPDFPTI
5N1Y 1.39 Å, HLA-A02 carrying MVWGPDPLYV
1I4F 1.4 Å, Crystal structure of HLA-A*0201/MAGE-A4-peptide complex
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
3MRB 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503…
3MRK 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with AFP137 nonapeptide
6J2A 1.4 Å, The structure of HLA-A*3003/NP44
1X7Q 1.45 Å, Crystal structure of HLA-A*1101 with sars nucleocapsid peptide

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