5H94: Swine MHC CLASSI for 1.48 angstroms

Crystal structure of Swine MHC CLASSI for 1.48 angstroms. Determined by X-ray diffraction at 1.48 Å resolution. Released 18 May 2016.

Method: X-ray diffraction
Resolution: 1.48 Å
Organisms: Sus scrofa, H1N1 swine influenza virus
Chains: 6
Atoms: 7,048
Mol. weight: 88.33 kDa
Released: 18 May 2016

Explore 5H94 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5H94 contains 30 α-helices and 60 β-strands across 5 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: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	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	51-53	3
α-helix	58-85	28
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	139-151	13
α-helix	154-160	7
α-helix	161-165	5
α-helix	166-175	10
α-helix	177-180	4
α-helix	183	1
β-strand	184	1	2
α-helix	185-186	2
β-strand	187-196	10	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	258-263	6	4
β-strand	271-273	3	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	5
α-helix	6-7	2
β-strand	8-13	6	6
β-strand	23-32	10	6
β-strand	33	1	5
β-strand	38-43	6	7
β-strand	46-47	2	7
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Chain D: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	8
α-helix	16-18	3
β-strand	20-29	10	8
β-strand	32-38	7	8
β-strand	47-48	2	8
α-helix	51-53	3
α-helix	58-85	28
β-strand	95-104	10	8
β-strand	110-119	10	8
β-strand	122-127	6	8
β-strand	134-136	3	8
α-helix	139-151	13
α-helix	154-160	7
α-helix	161-165	5
α-helix	166-175	10
α-helix	177-180	4
α-helix	183	1
β-strand	184	1	9
α-helix	185-186	2
β-strand	187-193	7	10
β-strand	200-209	10	10
β-strand	210	1	9
β-strand	215-220	6	11
β-strand	223-224	2	11
α-helix	226-228	3
β-strand	230-231	2	10
α-helix	232-234	3
β-strand	235-236	2	10
β-strand	242-250	9	10
α-helix	255-257	3
β-strand	258-263	6	11
β-strand	271-273	3	11

Chain E: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	12
α-helix	6-7	2
β-strand	8-13	6	13
β-strand	23-32	10	13
β-strand	33	1	12
β-strand	38-43	6	14
β-strand	46-47	2	14
β-strand	51-52	2	13
β-strand	56-57	2	13
β-strand	63-71	9	13
β-strand	79-84	6	14
β-strand	92-95	4	14

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, D	protein	275	Sus scrofa	A0A0N9JT91 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	98	Sus scrofa	Q07717 (AlphaFold model)
Nonapeptide from Influenza A virus HA protein	C, F	protein	9	H1N1 swine influenza virus	C4RUF0

Sequence of entity 1 (A, D), FASTA

>5H94_1 MHC class I antigen (chains A, D)
GPHSLSYFYTAVSRPDRGDSRFIAVGYVDDTQFVRFDSDAPNPREEPRAPWIQQEGQEYW
DRETQISKDNAQTYRVNLNNLRGYYNQSEAGSHTFQNMYGCYLGPDGLLLHGYHQYAYDG
ADYIALNEDLRSWTAADTAAQITKRKWEASGWAEQERSYLQGLCVESLREYLEMGKDTLQ
RAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDGT
FQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD

Sequence of entity 2 (B, E), FASTA

>5H94_2 Beta-2-microglobulin (chains B, E)
VARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWS
FYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH

Sequence of entity 3 (C, F), FASTA

>5H94_3 Nonapeptide from Influenza A virus HA protein (chains C, F)
KMNTQFTAV

Primary citation

Structural and Biochemical Analyses of Swine Major Histocompatibility Complex Class I Complexes and Prediction of the Epitope Map of Important Influenza A Virus Strains. Fan, S., Wu, Y., Wang, S. et al. J Virol (2016) 90:6625-6641. DOI 10.1128/JVI.00119-16 · PubMed

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