3WS3: H-2D

Crystal Structure of H-2D in complex with an insulin derived peptide. Determined by X-ray diffraction at 2.33 Å resolution. Released 26 Mar 2014.

Method: X-ray diffraction
Resolution: 2.33 Å
Organism: Mus musculus
Chains: 6
Atoms: 6,355
Mol. weight: 89.48 kDa
Released: 26 Mar 2014

Explore 3WS3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3WS3 contains 21 α-helices and 57 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: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	27-36	10	1
α-helix	44	1
β-strand	45-52	8	1
β-strand	55-61	7	1
β-strand	70-71	2	1
α-helix	74-78	5
α-helix	81-108	28
α-helix	111-112	2
β-strand	118-127	10	1
β-strand	133-142	10	1
β-strand	145-150	6	1
β-strand	157-159	3	1
α-helix	162-174	13
α-helix	176-185	10
α-helix	187-197	11
β-strand	207	1	2
α-helix	208-209	2
β-strand	210-217	8	3
β-strand	223-232	10	3
β-strand	233	1	2
β-strand	238-240	3	4
β-strand	253-254	2	3
β-strand	258-259	2	3
β-strand	265-273	9	3
β-strand	283-286	4	4
β-strand	294-296	3	4

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	5
β-strand	26-31	6	6
β-strand	41-50	10	6
β-strand	51	1	5
β-strand	56-61	6	7
β-strand	64-65	2	7
β-strand	70-71	2	6
α-helix	72-74	3
β-strand	75-76	2	6
β-strand	82-90	9	6
β-strand	98-103	6	7
β-strand	111-114	4	7

Chain C: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	27-36	10	8
β-strand	45-52	8	8
β-strand	55-61	7	8
β-strand	70-71	2	8
α-helix	74-78	5
α-helix	81-108	28
β-strand	118-127	10	8
β-strand	133-142	10	8
β-strand	145-150	6	8
β-strand	157-159	3	8
α-helix	162-173	12
α-helix	177-182	6
α-helix	183-187	5
α-helix	188-199	12
β-strand	207	1	9
α-helix	208-209	2
β-strand	210-217	8	10
β-strand	222-232	11	10
β-strand	233	1	9
β-strand	238-243	6	11
β-strand	246-248	3	11
β-strand	252-254	3	10
β-strand	258-259	2	10
β-strand	265-274	10	10
α-helix	278-280	3
β-strand	282-286	5	11
β-strand	294-296	3	11

Chain D: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
β-strand	26-31	6	12
α-helix	34-35	2
β-strand	41-50	10	12
β-strand	56-61	6	13
β-strand	64-65	2	13
α-helix	66	1
β-strand	70-71	2	12
α-helix	72-74	3
β-strand	75-76	2	12
β-strand	82-90	9	12
β-strand	98-103	6	13
β-strand	111-114	4	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-B alpha chain	A, C	protein	273	Mus musculus	P01899 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	100	Mus musculus	P01887 (AlphaFold model)
Insulin derived 9-mer peptide	E, F	protein	9		P01325 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3WS3_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A, C)
PHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWE
RETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGR
DYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLLR
TDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTF
QKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRW

Sequence of entity 2 (B, D), FASTA

>3WS3_2 Beta-2-microglobulin (chains B, D)
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (E, F), FASTA

>3WS3_3 Insulin derived 9-mer peptide (chains E, F)
YQLENYCGL

Primary citation

Compensatory mechanisms allow undersized anchor-deficient class I MHC ligands to mediate pathogenic autoreactive T cell responses. Lamont, D., Mukherjee, G., Kumar, P.R. et al. J Immunol (2014) 193:2135-2146. DOI 10.4049/jimmunol.1400997 · 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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