3QQ3: MHC class I antigen

Crystal structure of swine major histocompatibility complex class I SLA-1 0401 and identification of 2009 pandemic swine-origin influenza A H1N1 virus cytotoxic T lymphocyte epitope peptides. Determined by X-ray diffraction at 2.59 Å resolution. Released 28 Dec 2011.

Method: X-ray diffraction
Resolution: 2.59 Å
Organisms: Sus scrofa, Influenza A virus
Chains: 6
Atoms: 6,593
Mol. weight: 88.88 kDa
Released: 28 Dec 2011

Explore 3QQ3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QQ3 contains 28 α-helices and 60 β-strands across 6 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	1
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	57-84	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	138-150	13
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
α-helix	195-197	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	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	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
α-helix	48	1
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 C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Chain D: 11 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	50-52	3
α-helix	57-84	28
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
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	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	199-208	10	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	229-230	2	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

Chain E: 2 helices, 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
α-helix	53-55	3
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	O19244 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	100	Sus scrofa	Q07717 (AlphaFold model)
9-mer peptide from Neuraminidase	C, F	protein	9	Influenza A virus	Q9Q0U7

Sequence of entity 1 (A, D), FASTA

>3QQ3_1 MHC class I antigen (chains A, D)
GPHSLSYFYTAVSRPDRGDSRFIAVGYVDDTQFVRFDNYAPNPRMEPRVPWIQQEGQEYW
DRETRNVKETAQTYGVGLNTLRGYYNQSEAGSHTLQSMYGCYLGPDGLLLHGYRQDAYDG
ADYIALNEDLRSWTAADMAAQITKRKWEAADEAERRRSYLQGLCVESLRRYLEMGKDTLQ
RAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDGT
FQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD

Sequence of entity 2 (B, E), FASTA

>3QQ3_2 Beta-2-microglobulin (chains B, E)
EFVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKD
WSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH

Sequence of entity 3 (C, F), FASTA

>3QQ3_3 9-mer peptide from Neuraminidase (chains C, F)
NSDTVGWSW

Primary citation

Crystal structure of swine major histocompatibility complex class I SLA-1 0401 and identification of 2009 pandemic swine-origin influenza A H1N1 virus cytotoxic T lymphocyte epitope peptides. Zhang, N., Qi, J., Feng, S. et al. J Virol (2011) 85:11709-11724. DOI 10.1128/JVI.05040-11 · PubMed

Other PDB entries of the same protein (UniProt O19244 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3QQ4 2.1 Å, Crystal structure of swine major histocompatibility complex class I SLA-1 0401 and…
6LF8 2.5 Å, Crystal structure of pSLA-1*0401 complex with dodecapeptide RVEDVTNTAEYW

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