3WS6: H-2D

Crystal Structure of H-2D in complex with a mimotopic peptide. Determined by X-ray diffraction at 1.98 Å resolution. Released 26 Mar 2014.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Mus musculus
Chains: 6
Atoms: 6,973
Mol. weight: 91.32 kDa
Ligands: ZN
Released: 26 Mar 2014

Explore 3WS6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3WS6 contains 24 α-helices and 56 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: 9 helices, 19 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
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	187-203	17
β-strand	207	1	2
α-helix	208-209	2
β-strand	210-219	10	3
β-strand	222-232	11	3
β-strand	233	1	2
β-strand	238-243	6	4
β-strand	246-247	2	4
β-strand	253-254	2	3
α-helix	255-257	3
β-strand	258-259	2	3
β-strand	265-274	10	3
α-helix	278-280	3
β-strand	281-286	6	4
β-strand	294-296	3	4

Chain B: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	28-36	9	7
β-strand	45-52	8	7
β-strand	55-61	7	7
β-strand	70-71	2	7
α-helix	74-78	5
α-helix	81-108	28
β-strand	118-127	10	7
β-strand	133-142	10	7
β-strand	145-150	6	7
β-strand	157-159	3	7
α-helix	164-173	10
α-helix	176-182	7
α-helix	183-187	5
α-helix	188-203	16
β-strand	207	1	8
α-helix	208-209	2
β-strand	210-219	10	9
β-strand	222-232	11	9
β-strand	233	1	8
β-strand	238-243	6	10
β-strand	246-247	2	10
β-strand	253-254	2	9
α-helix	255-257	3
β-strand	258-259	2	9
β-strand	265-274	10	9
α-helix	278-280	3
β-strand	281-286	6	10
β-strand	294-296	3	10

Chain C: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	24-25	2
β-strand	26-31	6	11
β-strand	41-50	10	11
β-strand	56-61	6	12
β-strand	64-65	2	12
α-helix	66	1
β-strand	70-71	2	11
α-helix	72-74	3
β-strand	75-76	2	11
β-strand	82-90	9	11
β-strand	98-103	6	12
β-strand	111-114	4	12

Chain D: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	24-25	2
β-strand	26-31	6	5
β-strand	41-50	10	5
β-strand	56-61	6	6
β-strand	64-65	2	6
β-strand	70-71	2	5
α-helix	72-74	3
β-strand	75-76	2	5
β-strand	82-90	9	5
β-strand	98-103	6	6
α-helix	110	1
β-strand	111-114	4	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-B alpha chain	A, B	protein	275	Mus musculus	P01899 (AlphaFold model)
Beta-2-microglobulin	C, D	protein	100	Mus musculus	P01887 (AlphaFold model)
Mimotope 9-mer peptide	E, F	protein	9

Sequence of entity 1 (A, B), FASTA

>3WS6_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A, B)
PHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWE
RETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGR
DYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLLR
TDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTF
QKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEP

Sequence of entity 2 (C, D), FASTA

>3WS6_2 Beta-2-microglobulin (chains C, D)
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (E, F), FASTA

>3WS6_3 Mimotope 9-mer peptide (chains E, F)
YAIENYLEL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (SO4, GOL, IMD) are not listed.

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…

Browse structure collections

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