5W69: HLA-C*06:02 presenting ARFNDLRFV

HLA-C*06:02 presenting ARFNDLRFV. Determined by X-ray diffraction at 2.8 Å resolution. Released 23 Aug 2017.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, synthetic construct
Chains: 12
Atoms: 13,233
Mol. weight: 180.42 kDa
Released: 23 Aug 2017

Explore 5W69 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W69 contains 60 α-helices and 122 β-strands across 8 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	4-12	9	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	50-52	3
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	152-158	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

Chains B and D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	17	1	7
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	8
β-strand	44-45	2	8
α-helix	46	1
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	8
β-strand	91-94	4	8

Chain C: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	9
α-helix	20	1
β-strand	21-28	8	9
β-strand	31-37	7	9
β-strand	46-47	2	9
α-helix	50-53	4
α-helix	57-85	29
β-strand	94-103	10	9
β-strand	109-118	10	9
β-strand	121-126	6	9
β-strand	133-135	3	9
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	10
α-helix	184-185	2
β-strand	186-193	8	7
β-strand	198-208	11	7
β-strand	209	1	10
β-strand	214-219	6	11
β-strand	222-223	2	11
α-helix	225-227	3
β-strand	228-230	3	7
α-helix	231-233	3
β-strand	234-235	2	7
β-strand	241-250	10	7
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-272	3	11

Chain E: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	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	50-53	4
α-helix	57-85	29
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	140-149	10
α-helix	153-158	6
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
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	222-223	2	18
α-helix	225-227	3
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

Chains F and H: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	19
α-helix	4-5	2
β-strand	6-11	6	20
β-strand	21-30	10	20
β-strand	31	1	19
β-strand	36-41	6	21
β-strand	44-45	2	21
α-helix	46	1
β-strand	50-51	2	20
α-helix	52-54	3
β-strand	55-56	2	20
β-strand	62-70	9	20
β-strand	78-83	6	21
β-strand	91-94	4	21

Chain G: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	22
α-helix	20	1
β-strand	21-28	8	22
β-strand	31-37	7	22
β-strand	46-47	2	22
α-helix	50-53	4
α-helix	57-84	28
β-strand	94-102	9	22
β-strand	111-118	8	22
β-strand	121-126	6	22
β-strand	133-135	3	22
α-helix	138-150	13
α-helix	153-158	6
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	23
α-helix	184-185	2
β-strand	186-193	8	24
β-strand	198-208	11	24
β-strand	209	1	23
β-strand	214-219	6	25
β-strand	222-223	2	25
α-helix	225-227	3
β-strand	228-230	3	24
α-helix	231-233	3
β-strand	234-235	2	24
β-strand	241-250	10	24
α-helix	254-256	3
β-strand	257-262	6	25
β-strand	270-272	3	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, Cw-6 alpha chain	A, C, E, G	protein	276	Homo sapiens	P10321 (AlphaFold model)
Beta-2-microglobulin	B, D, F, H	protein	100	Homo sapiens	P61769 (AlphaFold model)
Ala-arg-phe-asn-asp-leu-arg-phe-val	I, J, K, L	protein	9	synthetic construct	Q13761 (AlphaFold model)

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

>5W69_1 HLA class I histocompatibility antigen, Cw-6 alpha chain (chains A, C, E, G)
CSHSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYW
DRETQKYKRQAQADRVNLRKLRGYYNQSEDGSHTLQWMYGCDLGPDGRLLRGYDQSAYDG
KDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQWRAYLEGTCVEWLRRYLENGKETLQ
RAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP

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

>5W69_2 Beta-2-microglobulin (chains B, D, F, H)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (I, J, K, L), FASTA

>5W69_3 ALA-ARG-PHE-ASN-ASP-LEU-ARG-PHE-VAL (chains I, J, K, L)
ARFNDLRFV

Primary citation

The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule. Mobbs, J.I., Illing, P.T., Dudek, N.L. et al. J Biol Chem (2017) 292:17203-17215. DOI 10.1074/jbc.M117.806976 · 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
4NT6 1.84 Å, HLA-C*0801 Crystal Structure
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…
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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