8FHU: PDB entry 8FHU

Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by H2-Dd. Determined by X-ray diffraction at 1.8 Å resolution. Released 28 Jun 2023.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 6,327
Mol. weight: 89.9 kDa
Released: 28 Jun 2023

Explore 8FHU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FHU contains 21 α-helices and 59 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, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	19-20	2
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	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-150	13
α-helix	152-161	10
α-helix	163-179	17
β-strand	183	1	2
β-strand	186-193	8	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 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: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
α-helix	20	1
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	57-84	28
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-150	13
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	199-208	10	10
β-strand	209	1	9
β-strand	214-218	5	11
β-strand	229-230	2	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-249	9	10
α-helix	254-256	3
β-strand	258-262	5	11
β-strand	270-273	4	11

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
α-helix	46	1
β-strand	50-51	2	13
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-D alpha chain	A, D	protein	277	Mus musculus	P01900 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	99	Mus musculus	P01887 (AlphaFold model)
Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial	C, F	protein	9	Homo sapiens	Q8NCN5 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8FHU_1 H-2 class I histocompatibility antigen, D-D alpha chain (chains A, D)
MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYW
ERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDG
CDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLL
RTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGT
FQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGKE

Sequence of entity 2 (B, E), FASTA

>8FHU_2 Beta-2-microglobulin (chains B, E)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (C, F), FASTA

>8FHU_3 Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial (chains C, F)
IGPRAVDVL

Primary citation

Structure of Pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented by H2-Dd. Custodio, J.M.F., Baker, B.M. To be published.

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…
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…
1BII 2.4 Å, The crystal structure of H-2DD MHC class I in complex with the HIV-1 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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