4NT6: HLA-C*0801 Crystal Structure

HLA-C*0801 Crystal Structure. Determined by X-ray diffraction at 1.84 Å resolution. Released 23 Jul 2014.

Method: X-ray diffraction
Resolution: 1.84 Å
Organisms: Homo sapiens, Influenza A virus (A/Boston/115JC/2009(H1N1))
Chains: 3
Atoms: 3,559
Mol. weight: 44.48 kDa
Released: 23 Jul 2014

Explore 4NT6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NT6 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: 12 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	50-53	4
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	152-158	7
α-helix	159-163	5
α-helix	164-174	11
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
α-helix	225-227	3
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	270-272	3	4

Chain B: 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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, Cw-8 alpha chain	A	protein	274	Homo sapiens	P10321 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
Matrix protein 1	C	protein	9	Influenza A virus (A/Boston/115JC/2009(H1N1))	D9J353

Sequence of entity 1 (A), FASTA

>4NT6_1 HLA class I histocompatibility antigen, Cw-8 alpha chain (chains A)
MSHSMRYFYTAVSRPGRGEPRFIAVGYVDDTQFVQFDSDAASPRGEPRAPWVEQEGPEYW
DRETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHTLQRMYGCDLGPDGRLLRGYNQFAYDG
KDYIALNEDLRSWTAADTAAQITQRKWEAARTAEQLRAYLEGTCVEWLRRYLENGKKTLQ
RAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRW

Sequence of entity 2 (B), FASTA

>4NT6_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRD

Sequence of entity 3 (C), FASTA

>4NT6_3 Matrix protein 1 (chains C)
GILGFVFTL

Primary citation

The immunodominant influenza A virus M158-66 cytotoxic T lymphocyte epitope exhibits degenerate class I major histocompatibility complex restriction in humans. Choo, J.A., Liu, J., Toh, X. et al. J Virol (2014) 88:10613-10623. DOI 10.1128/JVI.00855-14 · PubMed

Other PDB entries of the same protein (UniProt P10321 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6JTO 1.7 Å, Crystal structure of HLA-C05 in complex with a tumor mut10m peptide
5W6A 1.74 Å, HLA-C*06:02 presenting ARTELYRSL
5W67 2.3 Å, HLA-C*06:02 presenting VRSRR(ABA)LRL
5VGD 2.32 Å, Crystal Structure of HLA-C*0501 in complex with SAE
3BZF 2.5 Å, The human non-classical major histocompatibility complex molecule HLA-E
6PAG 2.5 Å, Killer cell immunoglobulin-like receptor 2DL3 in complex with HLA-C*07:02
5VGE 2.6 Å, Crystal structure of HLA-C*07:02 in complex with RYR peptide
1QQD 2.7 Å, Crystal structure of HLA-CW4, a ligand for the KIR2D natural killer cell inhibitory…
1IM9 2.8 Å, Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1 bound to…
5W69 2.8 Å, HLA-C*06:02 presenting ARFNDLRFV
1EFX 3.0 Å, Structure of a complex between the human natural killer cell receptor KIR2DL2 and a…
6PA1 3.01 Å, Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*07:02

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