5YLX: MHC class I antigen

Integrated illustration of a valid epitope based on the SLA class I structure and tetramer technique could carry forward the development of molecular vaccine in swine species. Determined by X-ray diffraction at 2.2 Å resolution. Released 24 Oct 2018.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Sus scrofa, Porcine reproductive and respiratory syndrome virus
Chains: 3
Atoms: 3,435
Mol. weight: 43.89 kDa
Released: 24 Oct 2018

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

Secondary structure: helices and β-sheets

5YLX 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-14	11	1
α-helix	15-17	3
β-strand	19-28	10	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
α-helix	57-85	29
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	138-149	12
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	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	223	1	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-248	8	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 3 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
α-helix	46-47	2
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	275	Sus scrofa	H6TIB1 (AlphaFold model)
Beta-2-microglobulin	B	protein	98	Sus scrofa	Q07717 (AlphaFold model)
PRRSV-NSP9-TMP9 peptide	C	protein	9	Porcine reproductive and respiratory syndrome virus	Q9YN02

Sequence of entity 1 (A), FASTA

>5YLX_1 MHC class I antigen (chains A)
GPHSLSYFSTAVSRPDRGDSRFIAVGYVDDTQFVRFDSDAPNPRMEPRVPWIQQEGQEYW
AEETRKVKDNAQTYRVNLKALRGYYNQSVAGSHTLQSMFGCYLGPDGLLLHGYRQDAYDG
ADYIALNEDLRSWTAADMAAQITKRKWEAADAAEQMRSYLQGLCVESLRKYLEMGKDTLQ
RAEPPKTHVTRHPSSDLGATLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDGT
FQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD

Sequence of entity 2 (B), FASTA

>5YLX_2 Beta-2-microglobulin (chains B)
VARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWS
FYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH

Sequence of entity 3 (C), FASTA

>5YLX_3 PRRSV-NSP9-TMP9 peptide (chains C)
TMPPGFELY

Primary citation

Illumination of PRRSV Cytotoxic T Lymphocyte Epitopes by the Three-Dimensional Structure and Peptidome of Swine Lymphocyte Antigen Class I (SLA-I). Pan, X., Zhang, N., Wei, X. et al. Front Immunol (2019) 10:2995-2995. DOI 10.3389/fimmu.2019.02995 · PubMed

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