1FYT: PDB entry 1FYT

Crystal structure of a complex of a human alpha/beta-T cell receptor, influenza ha antigen peptide, and MHC class II molecule, HLA-DR1. Determined by X-ray diffraction at 2.6 Å resolution. Released 8 Nov 2000.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, H3N2 subtype
Chains: 5
Atoms: 6,644
Mol. weight: 96.71 kDa
Ligands: NAG
Released: 8 Nov 2000

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

Secondary structure: helices and β-sheets

1FYT contains 23 α-helices and 77 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: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	10	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	48-51	4
β-strand	53	1	2
α-helix	57-76	20
α-helix	80-84	5
β-strand	85	1	3
β-strand	88-93	6	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	5
β-strand	126-128	3	5
β-strand	133-134	2	4
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	5
β-strand	174-179	6	5

Chain B: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-72	8
α-helix	74	1
α-helix	75-79	5
α-helix	80-86	7
β-strand	95	1	6
α-helix	96-97	2
β-strand	98-103	6	7
β-strand	115-122	8	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136-138	3	8
β-strand	142-144	3	7
β-strand	148-149	2	7
β-strand	155-161	7	7
β-strand	171-176	6	8
β-strand	184-188	5	8

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	307	1	2
α-helix	312-317	6

Chain D: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	9
β-strand	9-13	5	10
α-helix	17	1
β-strand	18-20	3	9
β-strand	23-25	3	9
β-strand	31-37	7	10
β-strand	44-49	6	10
β-strand	55-57	3	9
α-helix	59-61	3
β-strand	63-67	5	9
β-strand	72-77	6	9
α-helix	82-84	3
β-strand	86-93	8	10
β-strand	104-106	3	10
β-strand	110-115	6	10
α-helix	116	1
β-strand	124-128	5	11
β-strand	137-142	6	11
β-strand	159-160	2	11
β-strand	164-168	5	11
α-helix	169-171	3
β-strand	173-182	10	11
α-helix	189-192	4
β-strand	202	1	11

Chain E: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	12
β-strand	10-14	5	13
β-strand	19-21	3	14
β-strand	24-25	2	12
β-strand	31-38	8	13
β-strand	42-49	8	13
β-strand	56-57	2	13
β-strand	65-68	4	14
β-strand	74	1	12
β-strand	76-79	4	14
α-helix	84-86	3
β-strand	88-95	8	13
β-strand	107-108	2	13
β-strand	109	1	12
β-strand	112-117	6	13
α-helix	120-122	3
β-strand	124	1	15
β-strand	127-131	5	16
α-helix	132-134	3
α-helix	135-141	7
β-strand	143-153	11	16
β-strand	154	1	15
β-strand	158-164	7	17
β-strand	167-169	3	17
β-strand	173-175	3	16
β-strand	180-181	2	16
β-strand	191-200	10	16
α-helix	201-204	4
β-strand	210-217	8	17
β-strand	220	1	18
α-helix	231-232	2
β-strand	234	1	18
β-strand	236-243	8	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, dr alpha chain	A	protein	181	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, dr-1 beta chain	B	protein	192	Homo sapiens	P01911 (AlphaFold model)
Hemagglutinin HA1 peptide chain	C	protein	13	H3N2 subtype	P03437
T-cell receptor alpha chain	D	protein	212	Homo sapiens	P01848 (AlphaFold model)
T-cell receptor beta chain	E	protein	245	Homo sapiens	P01850

Sequence of entity 1 (A), FASTA

>1FYT_1 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
D

Sequence of entity 2 (B), FASTA

>1FYT_2 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR-1 BETA CHAIN (chains B)
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRARS

Sequence of entity 3 (C), FASTA

>1FYT_3 HEMAGGLUTININ HA1 PEPTIDE CHAIN (chains C)
PKYVKQNTLKLAT

Sequence of entity 4 (D), FASTA

>1FYT_4 T-CELL RECEPTOR ALPHA CHAIN (chains D)
QSVTQLGSHVSVSEGALVLLRCNYSSSVPPYLFWYVQYPNQGLQLLLKYTSAATLVKGIN
GFEAEFKKSETSFHLTKPSAHMSDAAEYFCAVSESPFGNEKLTFGTGTRLTIIPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESSCDVK

Sequence of entity 5 (E), FASTA

>1FYT_5 T-CELL RECEPTOR BETA CHAIN (chains E)
KVTQSSRYLVKRTGEKVFLECVQDMDHENMFWYRQDPGLGLRLIYFSYDVKMKEKGDIPE
GYSVSREKKERFSLILESASTNQTSMYLCASSSTGLPYGYTFGSGTRLTVVEDLNKVFPP
EVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPAL
NDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
DCGFT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structure of a covalently stabilized complex of a human alphabeta T-cell receptor, influenza HA peptide and MHC class II molecule, HLA-DR1. Hennecke, J., Carfi, A., Wiley, D.C. EMBO J (2000) 19:5611-5624. DOI 10.1093/emboj/19.21.5611 · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

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