5NPZ: MHC class I antigen

Porcine (Sus scrofa) Major Histocompatibility Complex, class I, presenting EFEDLTFLA. Determined by X-ray diffraction at 1.43 Å resolution. Released 2 May 2018.

Method: X-ray diffraction
Resolution: 1.43 Å
Organisms: Sus scrofa, unidentified influenza virus
Chains: 3
Atoms: 3,862
Mol. weight: 45.02 kDa
Released: 2 May 2018

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

Secondary structure: helices and β-sheets

5NPZ contains 14 α-helices and 30 β-strands across 2 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	20-29	10	1
β-strand	32-38	7	1
β-strand	47-48	2	1
α-helix	51-55	5
α-helix	58-85	28
β-strand	95-104	10	1
α-helix	105	1
β-strand	110-119	10	1
β-strand	122-127	6	1
β-strand	134-136	3	1
α-helix	139-150	12
α-helix	153-160	8
α-helix	161-165	5
α-helix	166-175	10
α-helix	177-180	4
β-strand	184	1	2
α-helix	185-186	2
β-strand	187-195	9	3
β-strand	199-209	11	3
β-strand	210	1	2
β-strand	215-220	6	4
β-strand	223-224	2	4
α-helix	226-228	3
β-strand	230-231	2	3
α-helix	232-234	3
β-strand	235-236	2	3
β-strand	242-250	9	3
α-helix	255-257	3
β-strand	259-263	5	4
β-strand	271-273	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	49-50	2	6
α-helix	51-53	3
β-strand	54-55	2	6
β-strand	61-69	9	6
β-strand	77-82	6	7
β-strand	90-93	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	277	Sus scrofa	B1PJV3 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Sus scrofa	Q07717 (AlphaFold model)
Glu-phe-glu-asp-leu-thr-phe-leu-ala	C	protein	9	unidentified influenza virus	P03466 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5NPZ_1 MHC class I antigen (chains A)
MGPHSLSYFSTAVSRPDRGDSRFIAVGYVDDTQFVRFDSDAPNPRMEPRAPWIQQEGQEY
WDRNTRNVMGSAQINRVNLKTLRGYYNQSEAGSHTLQWMYGCYLGPDGLLLRGYDQFAYD
GADYLALNEDLRSWTAADMAAQISKRKWEAADAAEHWRSYLQGTCVESLRRYLQMGKDTL
QRAEPPKTHVTRHPSSDLGVTLRCWALGFHPKEISLTWQREGQDQSQDMELVETRPSGDG
TFQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWDP

Sequence of entity 2 (B), FASTA

>5NPZ_2 Beta-2-microglobulin (chains B)
MVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDW
SFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH

Sequence of entity 3 (C), FASTA

>5NPZ_3 GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA (chains C)
EFEDLTFLA

Primary citation

Induction of influenza-specific local CD8 T-cells in the respiratory tract after aerosol delivery of vaccine antigen or virus in the Babraham inbred pig. Tungatt, K., Dolton, G., Morgan, S.B. et al. PLoS Pathog (2018) 14:e1007017-e1007017. DOI 10.1371/journal.ppat.1007017 · PubMed

Other PDB entries of the same protein (UniProt B1PJV3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NQ0 1.1 Å, Porcine (Sus scrofa) Major Histocompatibility Complex, class I, presenting DFEREGYSL
5NQ3 1.57 Å, 'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro…
5NQ1 2.14 Å, Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro…

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