5E8O: PDB entry 5E8O

The structure of the TEIPP associated altered peptide ligand Trh4-p2ABU in complex with H-2D(b). Determined by X-ray diffraction at 1.98 Å resolution. Released 3 Feb 2016.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Mus musculus
Chains: 6
Atoms: 6,340
Mol. weight: 89.66 kDa
Released: 3 Feb 2016

Explore 5E8O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E8O contains 18 α-helices and 60 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: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	1
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	133-134	2	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	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

Chains B and E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain D: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	8
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	50-54	5
α-helix	57-84	28
α-helix	87-88	2
β-strand	93-103	11	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-134	2	8
α-helix	138-150	13
α-helix	152-161	10
α-helix	163-175	13
β-strand	183	1	9
β-strand	186-193	8	10
α-helix	195-197	3
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-223	2	11
β-strand	228-230	3	10
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-272	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-B alpha chain	A, D	protein	276	Mus musculus	P01899 (AlphaFold model)
Ceramide synthase 5	C, F	protein	9	Mus musculus	Q9D6K9 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	99	Mus musculus	P01887 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5E8O_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A, D)
GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW
ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEG
RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEP

Sequence of entity 2 (C, F), FASTA

>5E8O_2 Ceramide synthase 5 (chains C, F)
MALRMTAVM

Sequence of entity 3 (B, E), FASTA

>5E8O_3 Beta-2-microglobulin (chains B, E)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Primary citation

The MHC Class I Cancer-Associated Neoepitope Trh4 Linked with Impaired Peptide Processing Induces a Unique Noncanonical TCR Conformer. Hafstrand, I., Doorduijn, E.M., Duru, A.D. et al. J Immunol (2016) 196:2327-2334. DOI 10.4049/jimmunol.1502249 · 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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