6PAG: Killer cell immunoglobulin-like receptor 2DL3

Killer cell immunoglobulin-like receptor 2DL3 in complex with HLA-C*07:02. Determined by X-ray diffraction at 2.5 Å resolution. Released 16 Dec 2020.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 4,478
Mol. weight: 67.18 kDa
Released: 16 Dec 2020

Explore 6PAG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PAG contains 19 α-helices and 47 β-strands across 4 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: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	1
α-helix	15-17	3
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	57-84	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	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
α-helix	184-185	2
β-strand	186-195	10	2
β-strand	198-208	11	2
β-strand	213-219	7	3
β-strand	222-223	2	3
α-helix	224-226	3
β-strand	229-230	2	2
α-helix	231-233	3
β-strand	234-235	2	2
β-strand	241-249	9	2
α-helix	254-256	3
β-strand	257-263	7	3
α-helix	269	1
β-strand	270-272	3	3

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	4
α-helix	4-5	2
β-strand	6-11	6	5
β-strand	21-30	10	5
β-strand	31	1	4
β-strand	36-41	6	6
β-strand	44-45	2	6
β-strand	50-51	2	5
β-strand	55-56	2	5
β-strand	62-70	9	5
β-strand	78-83	6	6
α-helix	90	1
β-strand	91-94	4	6

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Chain D: 2 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	7
β-strand	17-19	3	8
β-strand	24-30	7	7
β-strand	36-42	7	9
β-strand	47-52	6	9
β-strand	54-56	3	7
β-strand	59-66	8	7
α-helix	71-73	3
β-strand	75-80	6	9
α-helix	92-96	5
β-strand	97-99	3	9
β-strand	100-102	3	8
β-strand	109-112	4	10
β-strand	126-130	5	10
β-strand	136-139	4	8
β-strand	149-150	2	8
β-strand	153-154	2	10
β-strand	160-162	3	10
β-strand	177-181	5	8
β-strand	184-188	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, Cw-7 alpha chain	A	protein	278	Homo sapiens	P10321 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Arg-tyr-arg-pro-gly-thr-val-ala-leu	C	protein	9	synthetic construct	P68431 (AlphaFold model)
Killer cell immunoglobulin-like receptor 2DL3	D	protein	204	Homo sapiens	P43628 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6PAG_1 HLA class I histocompatibility antigen, Cw-7 alpha chain (chains A)
CSHSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYW
DRETQKYKRQAQADRVSLRNLRGYYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDG
KDYIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQ
RAEPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSS

Sequence of entity 2 (B), FASTA

>6PAG_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6PAG_3 ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEU (chains C)
RYRPGTVAL

Sequence of entity 4 (D), FASTA

>6PAG_4 Killer cell immunoglobulin-like receptor 2DL3 (chains D)
HEGVHRKPSLLAHPGPLVKSEETVILQCWSDVRFQHFLLHREGKFKDTLHLIGEHHDGVS
KANFSIGPMMQDLAGTYRCYGSVTHSPYQLSAPSDPLDIVITGLYEKPSLSAQPGPTVLA
GESVTLSCSSRSSYDMYHLSREGEAHERRFSAGPKVNGTFQADFPLGPATHGGTYRCFGS
FRDSPYEWSNSSDPLLVSVTGNPS

Primary citation

Structural plasticity of KIR2DL2 and KIR2DL3 enables altered docking geometries atop HLA-C. Moradi, S., Stankovic, S., O'Connor, G.M. et al. Nat Commun (2021) 12:2173-2173. DOI 10.1038/s41467-021-22359-x · 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
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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