5NQ1: MHC class I antigen

Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro globulin, presenting DFEREGYSL. Determined by X-ray diffraction at 2.14 Å resolution. Released 25 Apr 2018.

Method: X-ray diffraction
Resolution: 2.14 Å
Organisms: Sus scrofa, Homo sapiens, unidentified influenza virus
Chains: 6
Atoms: 6,745
Mol. weight: 89.82 kDa
Released: 25 Apr 2018

Explore 5NQ1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NQ1 contains 28 α-helices and 62 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	1
α-helix	16-18	3
β-strand	20-29	10	1
β-strand	32-38	7	1
β-strand	47-48	2	1
α-helix	52-55	4
α-helix	58-86	29
β-strand	95-104	10	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	187-194	8	3
β-strand	200-209	10	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	229-231	3	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	258-263	6	4
β-strand	271-273	3	4

Chains B and E: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	3	1	6
α-helix	4-5	2
β-strand	6-11	6	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	36-41	6	8
β-strand	44-45	2	8
β-strand	50-51	2	7
α-helix	52-54	3
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-83	6	8
β-strand	91-94	4	8

Chain D: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	9
α-helix	16-18	3
β-strand	20-29	10	9
β-strand	32-38	7	9
β-strand	47-48	2	9
α-helix	52-55	4
α-helix	58-86	29
β-strand	95-104	10	9
β-strand	110-119	10	9
β-strand	122-127	6	9
β-strand	134-136	3	9
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	10
α-helix	185-186	2
β-strand	187-194	8	11
β-strand	200-209	10	11
β-strand	210	1	10
β-strand	215-220	6	12
β-strand	223-224	2	12
α-helix	226-228	3
β-strand	229-231	3	11
α-helix	232-234	3
β-strand	235-236	2	11
β-strand	242-250	9	11
α-helix	255-257	3
β-strand	258-263	6	12
β-strand	271-273	3	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, D	protein	276	Sus scrofa	B1PJV3 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	100	Homo sapiens	P61769 (AlphaFold model)
Asp-phe-glu-arg-glu-gly-tyr-ser-leu	C, F	protein	9	unidentified influenza virus	Q9Q0U8

Sequence of entity 1 (A, D), FASTA

>5NQ1_1 MHC class I antigen (chains A, D)
MGPHSLSYFSTAVSRPDRGDSRFIAVGYVDDTQFVRFDSDAPNPRMEPRAPWIQQEGQEY
WDRNTRNVMGSAQINRVNLKTLRGYYNQSEAGSHTLQWMYGCYLGPDGLLLRGYDQFAYD
GADYLALNEDLRSWTAADMAAQISKRKWEAADAAEHWRSYLQGTCVESLRRYLQMGKDTL
QRAEPPKTHVTRHPSSDLGVTLRCWALGFHPKEISLTWQREGQDQSQDMELVETRPSGDG
TFQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD

Sequence of entity 2 (B, E), FASTA

>5NQ1_2 Beta-2-microglobulin (chains B, E)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F), FASTA

>5NQ1_3 ASP-PHE-GLU-ARG-GLU-GLY-TYR-SER-LEU (chains C, F)
DFEREGYSL

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
5NPZ 1.43 Å, Porcine (Sus scrofa) Major Histocompatibility Complex, class I, presenting EFEDLTFLA
5NQ3 1.57 Å, 'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro…

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