1BD2: HLA-a 0201

Complex between human T-cell receptor B7, viral peptide (TAX) and MHC class I molecule HLA-a 0201. Determined by X-ray diffraction at 2.5 Å resolution. Released 19 Aug 1998.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, Human T-lymphotropic virus 1
Chains: 5
Atoms: 6,378
Mol. weight: 94.86 kDa
Released: 19 Aug 1998

Explore 1BD2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1BD2 contains 22 α-helices and 74 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	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	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
β-strand	186-192	7	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
α-helix	225-227	3
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	253-256	4
β-strand	257-262	6	4
β-strand	270-273	4	4

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
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
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain D: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	8
β-strand	9-13	5	9
β-strand	18-24	7	8
β-strand	31-37	7	9
β-strand	44-50	7	9
β-strand	54A-57	4	8
β-strand	62-67	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-93	8	9
β-strand	104-106	3	9
β-strand	110-115	6	9
α-helix	116-118	3
β-strand	124-128	5	10
β-strand	130	1	11
β-strand	138-142	5	10
β-strand	159-160	2	10
α-helix	161-163	3
β-strand	164-167	4	10
β-strand	174-181	8	10
α-helix	189-192	4
β-strand	201	1	10

Chain E: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-21	3	14
β-strand	22-25	4	12
β-strand	31-37	7	13
β-strand	43-51	9	13
β-strand	54-57	4	13
β-strand	65-67	3	14
β-strand	74	1	12
β-strand	77-79	3	14
α-helix	84-86	3
β-strand	88-96	9	13
α-helix	97-99	3
β-strand	101-108	6	13
β-strand	112-117	6	13
α-helix	120-122	3
β-strand	124	1	15
β-strand	127-131	5	11
α-helix	132-134	3
α-helix	135-141	7
β-strand	143-153	11	11
β-strand	154	1	15
β-strand	158-164	7	16
β-strand	167-169	3	16
β-strand	173-175	3	11
α-helix	179	1
β-strand	180-181	2	11
β-strand	191-200	10	11
α-helix	201-204	4
β-strand	210-217	8	16
β-strand	220	1	17
α-helix	231-232	2
β-strand	234	1	17
β-strand	236-243	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA-a 0201	A	protein	275	Homo sapiens	P04439 (AlphaFold model)
Beta-2 microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Tax peptide	C	protein	9	Human T-lymphotropic virus 1	P0C213
T cell receptor alpha	D	protein	204	Homo sapiens	P01848 (AlphaFold model), P04437
T cell receptor beta	E	protein	244	Homo sapiens	A0A0K0K1A5, A0A5B9

Sequence of entity 1 (A), FASTA

>1BD2_1 HLA-A 0201 (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>1BD2_2 BETA-2 MICROGLOBULIN (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>1BD2_3 TAX PEPTIDE (chains C)
LLFGYPVYV

Sequence of entity 4 (D), FASTA

>1BD2_4 T CELL RECEPTOR ALPHA (chains D)
QQVKQNSPSLSVQEGRISILNCDYTNSMFDYFLWYKKYPAEGPTFLISISSIKDKNADGR
FTVFLNKSAKHLSLHIVPSQPGDSAVYFCAAMEGAQKLVFGQGTRLTINPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>1BD2_5 T CELL RECEPTOR BETA (chains E)
NAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEV
PNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYPGGGFYEQYFGPGTRLTVTEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Primary citation

Two human T cell receptors bind in a similar diagonal mode to the HLA-A2/Tax peptide complex using different TCR amino acids. Ding, Y.H., Smith, K.J., Garboczi, D.N. et al. Immunity (1998) 8:403-411. DOI 10.1016/S1074-7613(00)80546-4 · 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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