1JUF: H2-Db major histocompatibility antigen

Structure of Minor Histocompatibility Antigen peptide, H13b, complexed to H2-Db. Determined by X-ray diffraction at 2.0 Å resolution. Released 20 Mar 2002.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,442
Mol. weight: 44.88 kDa
Released: 20 Mar 2002

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

Secondary structure: helices and β-sheets

1JUF contains 10 α-helices and 30 β-strands across 2 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	1
α-helix	18-20	3
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
α-helix	57-84	28
β-strand	93-103	11	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-150	13
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	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
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-250	10	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	1003	1	5
β-strand	1006-1011	6	6
β-strand	1021-1030	10	6
β-strand	1031	1	5
β-strand	1036-1041	6	7
β-strand	1044-1045	2	7
α-helix	1046	1
β-strand	1050-1051	2	6
α-helix	1052-1054	3
β-strand	1055-1056	2	6
β-strand	1062-1070	9	6
β-strand	1078-1083	6	7
β-strand	1091-1094	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H2-Db major histocompatibility antigen	A	protein	276	Mus musculus	P01899 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Mus musculus	P01887 (AlphaFold model)
H13b peptide	C	protein	9	Mus musculus	Q9D8V0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1JUF_1 H2-Db major histocompatibility antigen (chains A)
GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW
ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEG
RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWER

Sequence of entity 2 (B), FASTA

>1JUF_2 Beta-2-microglobulin (chains B)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (C), FASTA

>1JUF_3 H13b peptide (chains C)
SSVIGVWYL

Primary citation

How H13 histocompatibility peptides differing by a single methyl group and lacking conventional MHC binding anchor motifs determine self-nonself discrimination. Ostrov, D.A., Roden, M.M., Shi, W. et al. J Immunol (2002) 168:283-289. DOI 10.4049/jimmunol.168.1.283 · PubMed

Other PDB entries of the same protein (UniProt P01899 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WZY 1.5 Å, Structure of DbNA(10) peptides bound to H-2Db MHC-I
6X00 1.55 Å, Structure of DbNA(11) peptides bound to H-2Db MHC-I
7N9J 1.74 Å, Crystal structure of H2DB in complex with HSF2 melanoma neoantigen
5M02 1.75 Å, Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
7N5Q 1.76 Å, Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation
7N4K 1.85 Å, 6218 TCR in complex with H2-Db PA 224
7N5C 1.87 Å, 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond
6G9Q 1.89 Å, Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen…
1WBX 1.9 Å, Crystal structures of murine MHC class I H-2 db and kb molecules in complex with ctl…
4L8D 1.9 Å, Crystal structure of the H2Db in complex with the NP-N5D peptide
3CC5 1.91 Å, H-2Db complex with human gp100
5M00 1.95 Å, Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide…

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