1BII: H-2DD MHC class I

The crystal structure of H-2DD MHC class I in complex with the HIV-1 derived peptide P18-110. Determined by X-ray diffraction at 2.4 Å resolution. Released 14 Oct 1998.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,210
Mol. weight: 56.08 kDa
Released: 14 Oct 1998

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

Secondary structure: helices and β-sheets

1BII contains 10 α-helices and 29 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	3-14	12	1
β-strand	18-28	11	1
β-strand	32-37	6	1
β-strand	46-47	2	1
α-helix	52-54	3
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	140-150	11
α-helix	152-161	10
α-helix	163-174	12
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	214-219	6	4
β-strand	223	1	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	257-262	6	4
β-strand	270-272	3	4

Chain B: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	303	1	5
α-helix	304-305	2
β-strand	306-311	6	6
β-strand	321-330	10	6
β-strand	331	1	5
β-strand	336-341	6	7
β-strand	344-345	2	7
α-helix	346	1
β-strand	350-356	7	6
β-strand	362-370	9	6
β-strand	378-383	6	7
β-strand	391-394	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I H-2DD	A	protein	365	Mus musculus	P01900 (AlphaFold model)
Beta-2 microglobulin	B	protein	119	Mus musculus	P01887 (AlphaFold model)
Decameric peptide	P	protein	10

Sequence of entity 1 (A), FASTA

>1BII_1 MHC CLASS I H-2DD (chains A)
MGAMAPRTLLLLLAAALGPTQTRAGSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRF
DSDAENPRYEPRARWIEQEGPEYWERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQ
WMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERD
RAYLEGECVEWLRRYLKNGNATLLRTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLT
WQLNGEELTQEMELVETRPAGDGTFQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGK
EEPPSSTKTNTVIIAVPVVLGAVVILGAVMAFVMKRRRNTGGKGGDYALAPGSQSSDMSL
PDCKV

Sequence of entity 2 (B), FASTA

>1BII_2 BETA-2 MICROGLOBULIN (chains B)
MARSVTLVFLVLVSLTGLYAIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQML
KNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (P), FASTA

>1BII_3 DECAMERIC PEPTIDE (chains P)
RGPGRAFVTI

Primary citation

The crystal structure of H-2Dd MHC class I complexed with the HIV-1-derived peptide P18-I10 at 2.4 A resolution: implications for T cell and NK cell recognition. Achour, A., Persson, K., Harris, R.A. et al. Immunity (1998) 9:199-208. DOI 10.1016/S1074-7613(00)80602-0 · PubMed

Other PDB entries of the same protein (UniProt P01900 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WEU 1.58 Å, Crystal Structure of H2-Dd with disulfide-linked 10mer peptide
3ECB 1.7 Å, Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human…
8FHU 1.8 Å, Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by…
5T7G 1.96 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
3E6H 2.1 Å, MHC CLASS I H-2Dd heavy chain complexed with Beta-2 Microglobulin and a variant peptide,…
5IVX 2.1 Å, Crystal Structure of B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex
8FHL 2.19 Å, Structure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented…
1QO3 2.3 Å, Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd
8D5F 2.31 Å, The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd
5KD7 2.35 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
6NPR 2.37 Å, Crystal structure of H-2Dd with C84-C139 disulfide in complex with gp120 derived peptide…
3E6F 2.41 Å, MHC CLASS I H-2Dd Heavy chain complexed with Beta-2 Microglobulin and a variant peptide,…

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