4L3E: PDB entry 4L3E

The complex between high affinity TCR DMF5(alpha-D26Y,beta-L98W) and human Class I MHC HLA-A2 with the bound MART-1(26-35)(A27L) peptide. Determined by X-ray diffraction at 2.56 Å resolution. Released 11 Jun 2014.

Method: X-ray diffraction
Resolution: 2.56 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,615
Mol. weight: 93.78 kDa
Released: 11 Jun 2014

Explore 4L3E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4L3E contains 21 α-helices and 76 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	15	1	2
β-strand	17	1	2
β-strand	21-28	8	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	3
α-helix	184-185	2
β-strand	186-193	8	4
β-strand	198-208	11	4
β-strand	209	1	3
β-strand	214-219	6	5
β-strand	222-223	2	5
β-strand	229-230	2	4
α-helix	231-233	3
β-strand	234-235	2	4
β-strand	241-250	10	4
β-strand	257-262	6	5
β-strand	270-272	3	5

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	6
α-helix	4-5	2
β-strand	6-11	6	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	35-41	7	8
β-strand	44-45	2	8
α-helix	46	1
β-strand	50-51	2	7
α-helix	52-54	3
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-84	7	8
β-strand	91-94	4	8

Chain D: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	9
β-strand	10-13	4	10
β-strand	18-24	7	9
β-strand	32-37	6	11
β-strand	44-49	6	11
β-strand	53-57	5	9
β-strand	60-65	6	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	85-91	7	11
β-strand	97-99	3	11
β-strand	103-104	2	11
β-strand	105-108	4	10
α-helix	109	1
β-strand	117-121	5	12
β-strand	122-123	2	13
β-strand	131-135	5	12
β-strand	152-153	2	12
β-strand	157-161	5	12
β-strand	166-174	9	12
β-strand	196	1	12

Chain E: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	14
β-strand	13-17	5	15
β-strand	22-24	3	16
β-strand	25-28	4	14
β-strand	34-41	8	15
β-strand	45-52	8	15
β-strand	59-60	2	15
β-strand	67-69	3	16
β-strand	76	1	14
β-strand	79-81	3	16
α-helix	86-88	3
β-strand	90-97	8	15
α-helix	103-104	2
β-strand	105-106	2	15
β-strand	110-115	6	15
α-helix	118-120	3
β-strand	122	1	17
α-helix	123-124	2
β-strand	125-130	6	13
α-helix	131-132	2
α-helix	133-139	7
β-strand	141-151	11	13
β-strand	152	1	17
β-strand	156-162	7	18
β-strand	165-167	3	18
β-strand	171-173	3	13
β-strand	189-198	10	13
α-helix	199-203	5
β-strand	208-215	8	18
β-strand	218	1	19
β-strand	232	1	19
β-strand	234-241	8	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A	protein	275	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	10	Homo sapiens	Q16655 (AlphaFold model)
DMF5 alpha chain	D	protein	199	Homo sapiens
DMF5 beta chain	E	protein	242	Homo sapiens

Sequence of entity 1 (A), FASTA

>4L3E_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>4L3E_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>4L3E_3 Melanoma antigen recognized by T-cells 1 (chains C)
ELAGIGILTV

Sequence of entity 4 (D), FASTA

>4L3E_4 DMF5 alpha chain (chains D)
KEVEQNSGPLSVPEGAIASLNCTYSYRGSQSFFWYRQYSGKSPELIMFIYSNGDKEDGRF
TAQLNKASQYVSLLIRDSQPSDSATYLCAVNFGGGKLIFGQGTELSVKPNIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPS

Sequence of entity 5 (E), FASTA

>4L3E_5 DMF5 beta chain (chains E)
IAGITQAPTSQILAAGRRMTLRCTQDMRHNAMYWYRQDLGLGLRLIHYSNTAGTTGKGEV
PDGYSVSRANTDDFPLTLASAVPSQTSVYFCASSWSFGTEAFFGQGTRLTVVEDLNKVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Primary citation

Computational design of the affinity and specificity of a therapeutic T cell receptor. Pierce, B.G., Hellman, L.M., Hossain, M. et al. PLoS Comput Biol (2014) 10:e1003478-e1003478. DOI 10.1371/journal.pcbi.1003478 · 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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