6D78: PDB entry 6D78

The complex between high-affinity TCR DMF5(alpha-D26Y,beta-L98W) and human Class I MHC HLA-A2 with the bound MART-1(27-35)peptide. Determined by X-ray diffraction at 2.35 Å resolution. Released 3 Apr 2019.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,708
Mol. weight: 94 kDa
Released: 3 Apr 2019

Explore 6D78 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D78 contains 21 α-helices and 73 β-strands across 4 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, 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	50-52	3
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
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-224	3	4
β-strand	228-230	3	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 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	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
α-helix	90	1
β-strand	91-94	4	7

Chain D: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	8
β-strand	10-13	4	9
β-strand	18-24	7	8
β-strand	32-37	6	9
β-strand	44-49	6	9
β-strand	53-57	5	8
β-strand	60-65	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-91	8	9
β-strand	97-99	3	9
β-strand	103-108	6	9
β-strand	117-122	6	10
β-strand	130-135	6	10
β-strand	152-153	2	10
α-helix	154-156	3
β-strand	157-161	5	10
β-strand	166-174	9	10
β-strand	196	1	10

Chain E: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	11
β-strand	13-17	5	12
β-strand	22-24	3	13
β-strand	25-28	4	11
β-strand	34-41	8	12
β-strand	45-52	8	12
β-strand	59-60	2	12
β-strand	67-69	3	13
β-strand	76	1	11
β-strand	79-81	3	13
α-helix	86-88	3
β-strand	90-97	8	12
β-strand	105-106	2	12
β-strand	110-115	6	12
α-helix	118-120	3
β-strand	122	1	14
β-strand	125-129	5	15
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	15
β-strand	152	1	14
β-strand	156-162	7	16
β-strand	165-167	3	16
β-strand	171-173	3	15
α-helix	177	1
β-strand	178-179	2	15
α-helix	187-188	2
β-strand	189-198	10	15
α-helix	199-202	4
β-strand	208-215	8	16
β-strand	218	1	17
α-helix	229-230	2
β-strand	232	1	17
β-strand	234-241	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A	protein	276	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Melanoma antigen recognized by T-cells 1	C	protein	9	Homo sapiens	Q16655 (AlphaFold model)
DMF5 alpha chain,DMF5 alpha chain	D	protein	200	Homo sapiens	K7N5M3 (AlphaFold model)
DMF5 beta chain,DMF5 beta chain	E	protein	243	Homo sapiens	K7N5M4

Sequence of entity 1 (A), FASTA

>6D78_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>6D78_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6D78_3 Melanoma antigen recognized by T-cells 1 (chains C)
AAGIGILTV

Sequence of entity 4 (D), FASTA

>6D78_4 DMF5 alpha chain,DMF5 alpha chain (chains D)
MKEVEQNSGPLSVPEGAIASLNCTYSYRGSQSFFWYRQYSGKSPELIMFIYSNGDKEDGR
FTAQLNKASQYVSLLIRDSQPSDSATYLCAVNFGGGKLIFGQGTELSVKPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPS

Sequence of entity 5 (E), FASTA

>6D78_5 DMF5 beta chain,DMF5 beta chain (chains E)
MIAGITQAPTSQILAAGRRMTLRCTQDMRHNAMYWYRQDLGLGLRLIHYSNTAGTTGKGE
VPDGYSVSRANTDDFPLTLASAVPSQTSVYFCASSWSFGTEAFFGQGTRLTVVEDLNKVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Primary citation

Improving T Cell Receptor On-Target Specificity via Structure-Guided Design. Hellman, L.M., Foley, K.C., Singh, N.K. et al. Mol Ther (2019) 27:300-313. DOI 10.1016/j.ymthe.2018.12.010 · PubMed

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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