1YMM: TCR/HLA-DR2b/MBP-peptide complex

TCR/HLA-DR2b/MBP-peptide complex. Determined by X-ray diffraction at 3.5 Å resolution. Released 3 May 2005.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 5
Atoms: 5,789
Mol. weight: 98.52 kDa
Ligands: NAG
Released: 3 May 2005

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

Secondary structure: helices and β-sheets

1YMM contains 17 α-helices and 69 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: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	6-15	10	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	41-43	3	1
α-helix	46-50	5
β-strand	53	1	2
α-helix	57-76	20
α-helix	80-82	3
β-strand	85	1	3
β-strand	88	1	4
β-strand	91-93	3	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
α-helix	140	1
β-strand	145-153	9	4
β-strand	160-166	7	5
β-strand	174-179	6	5

Chain B: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	1
β-strand	12-18	7	1
α-helix	20-22	3
β-strand	23-25	3	1
β-strand	27-32	6	1
β-strand	35-41	7	1
β-strand	48-49	2	1
α-helix	52-54	3
α-helix	55-63	9
α-helix	66-74	9
α-helix	75-79	5
α-helix	80-86	7
α-helix	87-89	3
β-strand	95	1	6
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	142-143	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	88	1	2
α-helix	92-94	3

Chain D: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	9
β-strand	24	1	10
α-helix	28	1
β-strand	29-35	7	11
β-strand	48-50	3	11
β-strand	63	1	9
β-strand	66	1	10
α-helix	67-69	3
β-strand	71	1	10
β-strand	74	1	9
β-strand	88-93	6	11
β-strand	100-102	3	11

Chain E: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	12
β-strand	10-12	3	13
β-strand	20-21	2	14
β-strand	23-25	3	12
β-strand	32-38	7	13
β-strand	46-51	6	13
β-strand	58-59	2	13
β-strand	69	1	14
β-strand	79-80	2	14
β-strand	91-95	5	13
β-strand	114-116	3	13
α-helix	121-123	3
β-strand	125	1	15
β-strand	128-129	2	16
α-helix	133-135	3
α-helix	138-141	4
β-strand	146-150	5	17
β-strand	151-152	2	16
β-strand	154	1	18
β-strand	155	1	15
β-strand	159	1	19
β-strand	163-164	2	20
β-strand	176	1	17
β-strand	192	1	18
β-strand	195-199	5	17
β-strand	212-217	6	20
β-strand	218	1	19
β-strand	238-243	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A	protein	191	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DR beta chain	B	protein	198	Homo sapiens	P01911 (AlphaFold model)
MBP peptide	C	protein	23		P02686 (AlphaFold model)
T cell receptor alpha chain	D	protein	207	Homo sapiens	P01848 (AlphaFold model)
T-cell receptor beta chain	E	protein	249	Homo sapiens	P01850

Sequence of entity 1 (A), FASTA

>1YMM_1 HLA class II histocompatibility antigen, DR alpha chain (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DAPSPLPETTE

Sequence of entity 2 (B), FASTA

>1YMM_2 HLA class II histocompatibility antigen, DR beta chain (chains B)
GDTRPRFLWQPKRECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEY
WNSQKDILEQARAAVDTYCRHNYGVVESFTVQRRVQPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRARSESAQSK

Sequence of entity 3 (C), FASTA

>1YMM_3 MBP peptide (chains C)
ENPVVHFFKNIVTPRGGSGGGGG

Sequence of entity 4 (D), FASTA

>1YMM_4 T cell receptor alpha chain (chains D)
SQQGEEDPQALSIQEGENATMNCSYKTSINNLQWYRQNSGRGLVHLILIRSNEREKHSGR
LRVTLDTSKKSSSLLITASRAADTASYFCATDTTSGTYKYIFGTGTRLKVLANIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESSC

Sequence of entity 5 (E), FASTA

>1YMM_5 T-cell receptor beta chain (chains E)
GAVVSQHPSWVISKSGTSVKIECRSLDFQATTMFWYRQFPKQSLMLMATSNEGSKATYEQ
GVEKDKFLINHASLTLSTLTVTSAHPEDSSFYICSARDLTSGANNEQFFGPGTRLTVLED
LKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQP
LKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVS
AEAWGRADC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Unconventional topology of self peptide-major histocompatibility complex binding by a human autoimmune T cell receptor. Hahn, M., Nicholson, M.J., Pyrdol, J. et al. Nat Immunol (2005) 6:490-496. DOI 10.1038/ni1187 · 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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