8JV0: SLA-2*1001 allele and ASFV antigenic peptide

Crystal structure of the SLA-2*1001 allele and ASFV antigenic peptide at 2.2A resolution. Determined by X-ray diffraction at 2.2 Å resolution. Released 5 Jun 2024.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Sus scrofa, Asfivirus
Chains: 6
Atoms: 6,333
Mol. weight: 88.56 kDa
Released: 5 Jun 2024

Explore 8JV0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JV0 contains 24 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-14	11	1
β-strand	19-28	10	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
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	138-149	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	222-223	2	4
α-helix	225-227	3
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

Chains B and E: 1 helix, 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
β-strand	54-55	2	6
β-strand	61-69	9	6
β-strand	77-82	6	7
β-strand	90-93	4	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3

Chain D: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-14	11	8
β-strand	19-28	10	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	57-85	29
β-strand	94-104	11	8
β-strand	108-118	11	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-150	13
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-195	10	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-223	2	11
α-helix	225-227	3
β-strand	228-230	3	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	257-262	6	11
β-strand	270-272	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, D	protein	275	Sus scrofa	B1A9P1 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	98	Sus scrofa	Q07717 (AlphaFold model)
Tyr-met-asn-cys-ser-leu-pro-thr-tyr	C, F	protein	9	Asfivirus	P0C9J3

Sequence of entity 1 (A, D), FASTA

>8JV0_1 MHC class I antigen (chains A, D)
GPHSLSYFYTAVSRPDRGDSRFFIVGYVDDTQFVRFDSDAPNAKMEPRAQWIQQEGQEYW
DRETQISKDNAQINRVNLNTLRGYYNQSEAGSHTLQRMYGCYLGPDGLLLRGYDQDAYDG
ADYIALNEDLRSWTAADMAAQISKRKREAADEAERMRSYLQGRCVEWLQKYLEMGKDTLQ
RAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLSWQREGQDQSQDMELVETRPSGDGT
FQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD

Sequence of entity 2 (B, E), FASTA

>8JV0_2 Beta-2-microglobulin (chains B, E)
VARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWS
FYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH

Sequence of entity 3 (C, F), FASTA

>8JV0_3 TYR-MET-ASN-CYS-SER-LEU-PRO-THR-TYR (chains C, F)
YMNCSLPTY

Primary citation

Crystal structure of the SLA-2*1001 allele and ASFV antigenic peptide at 2.2A resolution. Wang, S. To be published.

Other PDB entries of the same protein (UniProt B1A9P1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8W6L 2.03 Å, Crystal structure of the SLA-2*1001 allele and ASFV antigenic peptide at 2.2A resolution

Browse structure collections

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