3QDM: PDB entry 3QDM

The complex between TCR DMF4 and human Class I MHC HLA-A2 with the bound MART-1(26-35)(A27L) decameric peptide. Determined by X-ray diffraction at 2.8 Å resolution. Released 6 Jul 2011.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,635
Mol. weight: 93.55 kDa
Released: 6 Jul 2011

Explore 3QDM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QDM contains 27 α-helices and 75 β-strands across 5 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	3-12	10	1
α-helix	20	1
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	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	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	213-219	7	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	241-250	10	3
α-helix	254-256	3
β-strand	257-263	7	4
β-strand	270-272	3	4

Chain B: 4 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
α-helix	90	1
β-strand	91-94	4	7

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7-8	2	8

Chain D: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	9
β-strand	4-6	3	10
β-strand	9-13	5	11
β-strand	18-23	6	10
β-strand	30-36	7	11
β-strand	42-48	7	11
β-strand	54-55	2	10
β-strand	60-64	5	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	84-91	8	11
β-strand	96-98	3	11
β-strand	99	1	9
β-strand	102-107	6	11
α-helix	108-109	2
β-strand	116-122	7	12
β-strand	129-134	6	12
β-strand	150-152	3	12
α-helix	153-155	3
β-strand	156-160	5	12
α-helix	161-163	3
β-strand	165-174	10	12
β-strand	194	1	12

Chain E: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	30-38	9	14
β-strand	42-51	10	14
β-strand	54-57	4	14
β-strand	65-67	3	13
β-strand	73-78	6	13
α-helix	83-85	3
β-strand	87-95	9	14
β-strand	97-98	2	8
α-helix	100-102	3
β-strand	103-104	2	14
β-strand	108-113	6	14
α-helix	116-118	3
β-strand	120	1	15
β-strand	123-128	6	12
α-helix	129-130	2
α-helix	131-137	7
β-strand	139-149	11	12
β-strand	150	1	15
β-strand	154-160	7	16
β-strand	163-165	3	16
β-strand	169-171	3	12
α-helix	175	1
β-strand	176-177	2	12
β-strand	187-196	10	12
α-helix	197-200	4
β-strand	206-213	8	16
β-strand	216	1	17
α-helix	227-228	2
β-strand	230	1	17
β-strand	232-239	8	16

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)
MART-1(27-35) peptide	C	protein	10		Q16655 (AlphaFold model)
DMF4 alpha chain	D	protein	195	Homo sapiens	P01848 (AlphaFold model)
DMF4 beta chain	E	protein	242	Homo sapiens

Sequence of entity 1 (A), FASTA

>3QDM_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>3QDM_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>3QDM_3 MART-1(27-35) peptide (chains C)
ELAGIGILTV

Sequence of entity 4 (D), FASTA

>3QDM_4 DMF4 alpha chain (chains D)
QLNQSPQSMFIQEGEDVSMNCTSSSIFNTWLWYKQDPGEGPVLLIALYKAGELTSNGRLT
AQFGITRKDSFLNISASIPSDVGIYFCAGGTGNQFYFGTGTSLTVIPNIQNPDPAVYQLR
DSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFAC
ANAFNNSIIPEDTFF

Sequence of entity 5 (E), FASTA

>3QDM_5 DMF4 beta chain (chains E)
AGITQSPRHKVTETGTPVTLRCHQTENHRYMYWYRQDPGHGLRLIHYSYGVKDTDKGEVS
DGYSVSRSKTEDFLLTLESATSSQTSVYFCAISEVGVGQPQHFGDGTRLSILEDLNKVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Primary citation

TCRs Used in Cancer Gene Therapy Cross-React with MART-1/Melan-A Tumor Antigens via Distinct Mechanisms. Borbulevych, O.Y., Santhanagopolan, S.M., Hossain, M. et al. J Immunol (2011) 187:2453-2463. DOI 10.4049/jimmunol.1101268 · 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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