1EFX: HLA-CW3

Structure of a complex between the human natural killer cell receptor KIR2DL2 and a class I MHC ligand HLA-CW3. Determined by X-ray diffraction at 3.0 Å resolution. Released 14 Jun 2000.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,411
Mol. weight: 89.03 kDa
Released: 14 Jun 2000

Explore 1EFX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1EFX contains 20 α-helices and 79 β-strands across 5 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	45-47	3	1
α-helix	50-53	4
α-helix	57-84	28
β-strand	94-104	11	1
β-strand	107-118	12	1
β-strand	122-126	5	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	186-192	7	2
β-strand	198-206	9	2
β-strand	208	1	3
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	229-230	2	2
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-242	2	3
β-strand	244-250	7	2
α-helix	253-256	4
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-22	2	7
β-strand	23-28	6	6
β-strand	31	1	5
β-strand	36-41	6	8
β-strand	44-45	2	8
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-67	6	6
β-strand	69-70	2	7
β-strand	78-83	6	8
β-strand	91-94	4	8

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Chain D: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	9-13	5	9
β-strand	17-19	3	10
β-strand	24-30	7	9
β-strand	36-42	7	11
β-strand	47-52	6	11
β-strand	54-56	3	9
β-strand	59-66	8	9
α-helix	71-73	3
β-strand	75-82	8	11
α-helix	93-96	4
β-strand	97-99	3	11
β-strand	100-102	3	10
β-strand	109-113	5	12
β-strand	117-118	2	13
β-strand	123-129	7	12
β-strand	130	1	14
β-strand	136-141	6	15
β-strand	148-151	4	15
β-strand	153-156	4	16
β-strand	159-161	3	16
β-strand	163-168	6	12
β-strand	173-181	9	15
β-strand	184-188	5	15
α-helix	190-194	5
β-strand	195-197	3	15
β-strand	198-199	2	13

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	9-13	5	17
β-strand	18-19	2	18
β-strand	24-30	7	17
β-strand	36-42	7	19
β-strand	47-52	6	19
β-strand	54-56	3	17
β-strand	59-66	8	17
α-helix	71-73	3
β-strand	75-82	8	19
α-helix	92-96	5
β-strand	97-99	3	19
β-strand	101-102	2	18
β-strand	109-113	5	20
β-strand	117-118	2	21
β-strand	123-129	7	20
β-strand	136-141	6	22
β-strand	148-151	4	22
α-helix	152	1
β-strand	153	1	23
β-strand	161	1	23
β-strand	163-168	6	20
β-strand	173-180	8	22
β-strand	181	1	24
β-strand	184	1	24
β-strand	187	1	18
α-helix	190-194	5
β-strand	195-197	3	22
β-strand	198-199	2	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA-CW3 (heavy chain)	A	protein	278	Homo sapiens	P10321 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Peptide from importin alpha-2	C	protein	9		P52292 (AlphaFold model)
Natural killer cell receptor KIR2DL2	D, E	protein	200	Homo sapiens	P43627 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1EFX_1 HLA-CW3 (HEAVY CHAIN) (chains A)
GSHSMRYFYTAVSRPGRGEPHFIAVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYW
DRETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHIIQRMYGCDVGPDGRLLRGYDQYAYDG
KDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQLRAYLEGLCVEWLRRYLKNGKETLQ
RAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQWDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEPSS

Sequence of entity 2 (B), FASTA

>1EFX_2 BETA-2-MICROGLOBULIN (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>1EFX_3 PEPTIDE FROM IMPORTIN ALPHA-2 (chains C)
GAVDPLLAL

Sequence of entity 4 (D, E), FASTA

>1EFX_4 NATURAL KILLER CELL RECEPTOR KIR2DL2 (chains D, E)
HEGVHRKPSLLAHPGRLVKSEETVILQCWSDVRFEHFLLHREGKFKDTLHLIGEHHDGVS
KANFSIGPMMQDLAGTYRCYGSVTHSPYQLSAPSDPLDIVITGLYEKPSLSAQPGPTVLA
GESVTLSCSSRSSYDMYHLSREGEAHECRFSAGPKVNGTFQADFPLGPATHGGTYRCFGS
FRDSPYEWSNSSDPLLVSVI

Primary citation

Crystal structure of an NK cell immunoglobulin-like receptor in complex with its class I MHC ligand. Boyington, J.C., Motyka, S.A., Schuck, P. et al. Nature (2000) 405:537-543. DOI 10.1038/35014520 · 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…
5W69 2.8 Å, HLA-C*06:02 presenting ARFNDLRFV
6PA1 3.01 Å, Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*07:02

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