4NQV: HLA A*0101

Crystal Structure of HLA A*0101 in complex with NP44, an 9-mer influenza epitope. Determined by X-ray diffraction at 2.39 Å resolution. Released 25 Dec 2013.

Method: X-ray diffraction
Resolution: 2.39 Å
Organisms: Homo sapiens, H7N9 subtype
Chains: 18
Atoms: 19,628
Mol. weight: 267.53 kDa
Released: 25 Dec 2013

Explore 4NQV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NQV contains 71 α-helices and 182 β-strands across 12 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.

Chains A and C: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	52-54	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	152-160	9
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
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-273	4	4

Chains B and D: 2 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
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain E: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	15
α-helix	20	1
β-strand	21-28	8	15
β-strand	31-37	7	15
β-strand	46-47	2	15
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	15
β-strand	109-118	10	15
β-strand	121-126	6	15
β-strand	133-135	3	15
α-helix	138-149	12
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
β-strand	183	1	16
α-helix	184-185	2
β-strand	186-193	8	17
β-strand	198-208	11	17
β-strand	209	1	16
β-strand	214-219	6	18
β-strand	222-224	3	18
β-strand	228-230	3	17
α-helix	231-233	3
β-strand	234-235	2	17
β-strand	241-250	10	17
α-helix	254-256	3
β-strand	257-262	6	18
β-strand	270-272	3	18

Chain F: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	19
α-helix	4-5	2
β-strand	6-11	6	20
β-strand	22-28	7	20
β-strand	31	1	19
β-strand	36-37	2	21
β-strand	55	1	20
β-strand	63-69	7	20
β-strand	81	1	22
β-strand	82-83	2	21
β-strand	92	1	22

Chain G: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	23
β-strand	21-28	8	23
β-strand	31-37	7	23
β-strand	46-47	2	23
α-helix	52-54	3
α-helix	57-84	28
β-strand	94-103	10	23
β-strand	109-118	10	23
β-strand	121-126	6	23
β-strand	133-135	3	23
α-helix	138-149	12
α-helix	152-160	9
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	24
β-strand	186-193	8	25
β-strand	198-208	11	25
β-strand	209	1	24
β-strand	214-219	6	26
β-strand	222-223	2	26
β-strand	228-230	3	25
α-helix	231-233	3
β-strand	234-235	2	25
β-strand	241-250	10	25
α-helix	254-256	3
β-strand	257-262	6	26
β-strand	270-272	3	26

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	27
α-helix	4-5	2
β-strand	6-11	6	28
β-strand	21-30	10	28
β-strand	31	1	27
β-strand	36-41	6	29
β-strand	44-46	3	29
β-strand	50-51	2	28
α-helix	52-54	3
β-strand	55-56	2	28
β-strand	62-70	9	28
β-strand	78-83	6	29
β-strand	91-94	4	29

Chain I: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	30
β-strand	21-28	8	30
β-strand	31-37	7	30
β-strand	46-47	2	30
α-helix	50-54	5
α-helix	57-84	28
β-strand	94-103	10	30
β-strand	109-118	10	30
β-strand	121-126	6	30
β-strand	133-135	3	30
α-helix	138-149	12
α-helix	152-160	9
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	31
α-helix	184-185	2
β-strand	186-193	8	32
β-strand	198-208	11	32
β-strand	209	1	31
β-strand	214-219	6	33
β-strand	222-223	2	33
β-strand	228-230	3	32
α-helix	231-233	3
β-strand	234-235	2	32
β-strand	241-250	10	32
α-helix	254-256	3
β-strand	257-262	6	33
β-strand	270-272	3	33

Chain J: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	34
α-helix	4-5	2
β-strand	6-11	6	35
β-strand	21-30	10	35
β-strand	31	1	34
β-strand	36-41	6	36
β-strand	44-45	2	36
α-helix	46	1
β-strand	50-51	2	35
α-helix	52-54	3
β-strand	55-56	2	35
β-strand	62-70	9	35
β-strand	78-83	6	36
β-strand	91-94	4	36

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-1 alpha chain	A, C, E, G, I, K	protein	274	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, D, F, H, J, L	protein	100	Homo sapiens	P61769 (AlphaFold model)
Nucleoprotein	M, N, O, P, Q, R	protein	9	H7N9 subtype	P03466 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>4NQV_1 HLA class I histocompatibility antigen, A-1 alpha chain (chains A, C, E, G, I, K)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYW
DQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDG
KDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

Sequence of entity 2 (B, D, F, H, J, L), FASTA

>4NQV_2 Beta-2-microglobulin (chains B, D, F, H, J, L)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (M, N, O, P, Q, R), FASTA

>4NQV_3 Nucleoprotein (chains M, N, O, P, Q, R)
CTELKLSDY

Primary citation

Preexisting CD8+ T-cell immunity to the H7N9 influenza A virus varies across ethnicities. Quinones-Parra, S., Grant, E., Loh, L. et al. Proc Natl Acad Sci U S A (2014) 111:1049-1054. DOI 10.1073/pnas.1322229111 · PubMed

Other PDB entries of the same protein (UniProt P04439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
3D25 1.3 Å, Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC…
3MRG 1.3 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081…
6JOZ 1.35 Å, Crystal structure of BRLF peptide from EBV in complex with HLA-A1101.
5C0G 1.37 Å, HLA-A02 carrying YLGGPDFPTI
5N1Y 1.39 Å, HLA-A02 carrying MVWGPDPLYV
1I4F 1.4 Å, Crystal structure of HLA-A*0201/MAGE-A4-peptide complex
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
3MRB 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503…
3MRK 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with AFP137 nonapeptide
6J2A 1.4 Å, The structure of HLA-A*3003/NP44
1X7Q 1.45 Å, Crystal structure of HLA-A*1101 with sars nucleocapsid peptide

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