5E8N: TEIPP associated Trh4 peptide

The structure of the TEIPP associated Trh4 peptide in complex with H-2D(b). Determined by X-ray diffraction at 2.25 Å resolution. Released 3 Feb 2016.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Mus musculus
Chains: 12
Atoms: 12,495
Mol. weight: 179.58 kDa
Released: 3 Feb 2016

Explore 5E8N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E8N contains 38 α-helices and 117 β-strands across 9 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, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	51-54	4
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	140-149	10
α-helix	152-161	10
α-helix	163-174	12
α-helix	183-185	3
β-strand	186-193	8	2
β-strand	198-208	11	2
β-strand	214-219	6	3
β-strand	222-223	2	3
β-strand	229-230	2	2
β-strand	234-235	2	2
β-strand	241-250	10	2
α-helix	254-256	3
β-strand	257-262	6	3
β-strand	270-273	4	3

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

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

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Chain D: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	7
β-strand	21-28	8	7
β-strand	31-37	7	7
β-strand	46-47	2	7
α-helix	50-54	5
α-helix	57-84	28
β-strand	93-103	11	7
β-strand	109-118	10	7
β-strand	121-126	6	7
β-strand	133-135	3	7
α-helix	140-149	10
α-helix	152-161	10
α-helix	163-173	11
β-strand	183	1	8
α-helix	184-185	2
β-strand	186-193	8	9
β-strand	198-208	11	9
β-strand	209	1	8
β-strand	214-219	6	10
β-strand	223	1	10
β-strand	229-230	2	9
β-strand	234-235	2	9
β-strand	241-250	10	9
β-strand	257-262	6	10
β-strand	270-272	3	10

Chain G: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	14
β-strand	21-28	8	14
β-strand	31-37	7	14
β-strand	46-47	2	14
α-helix	50-54	5
α-helix	57-84	28
β-strand	93-103	11	14
β-strand	109-118	10	14
β-strand	121-126	6	14
β-strand	133-134	2	14
α-helix	140-149	10
α-helix	152-161	10
α-helix	163-173	11
β-strand	183	1	15
α-helix	184-185	2
β-strand	186-193	8	16
β-strand	199-208	10	16
β-strand	209	1	15
β-strand	214-219	6	17
β-strand	223	1	17
β-strand	228-230	3	16
β-strand	234-235	2	16
β-strand	241-249	9	16
β-strand	257-262	6	17
β-strand	270-272	3	17

Chain H: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	18
α-helix	4-5	2
β-strand	6-11	6	19
β-strand	21-30	10	19
β-strand	31	1	18
β-strand	36-41	6	20
β-strand	44-45	2	20
α-helix	46	1
β-strand	50-51	2	19
α-helix	52-54	3
β-strand	55-56	2	19
β-strand	62-70	9	19
β-strand	78-83	6	20
β-strand	91-94	4	20

Chain J: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	21
α-helix	20	1
β-strand	21-28	8	21
β-strand	31-37	7	21
β-strand	46-47	2	21
α-helix	50-52	3
α-helix	57-84	28
β-strand	93-103	11	21
β-strand	109-118	10	21
β-strand	121-126	6	21
β-strand	133-134	2	21
α-helix	140-149	10
α-helix	152-161	10
α-helix	163-173	11
β-strand	183	1	22
α-helix	184-185	2
β-strand	186-190	5	23
β-strand	202-208	7	23
β-strand	209	1	22
β-strand	213-218	6	24
β-strand	230	1	23
β-strand	234-235	2	23
β-strand	241-246	6	23
α-helix	254-256	3
β-strand	258-263	6	24
β-strand	270-272	3	24

Chain K: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	25
α-helix	4-5	2
β-strand	6-11	6	26
β-strand	21-30	10	26
β-strand	31	1	25
β-strand	35-41	7	27
β-strand	44-45	2	27
β-strand	50-51	2	26
α-helix	52-54	3
β-strand	55-56	2	26
β-strand	62-70	9	26
β-strand	79-84	6	27
β-strand	91-94	4	27

Molecules and chains

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

Sequence of entity 1 (A, D, G, J), FASTA

>5E8N_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A, D, G, J)
GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW
ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEG
RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEP

Sequence of entity 2 (B, E, H, K), FASTA

>5E8N_2 Beta-2-microglobulin (chains B, E, H, K)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (C, F, I, L), FASTA

>5E8N_3 Ceramide synthase 5 (chains C, F, I, L)
MCLRMTAVM

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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