9BL9: KIR3DL1*114

KIR3DL1*114 in complex with HLA-A*24:02 presenting the NEF peptide. Determined by X-ray diffraction at 2.6 Å resolution. Released 13 Nov 2024.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Human immunodeficiency virus
Chains: 4
Atoms: 5,122
Mol. weight: 79.04 kDa
Ligands: NAG
Released: 13 Nov 2024

Explore 9BL9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BL9 contains 20 α-helices and 62 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	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	93-103	11	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
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	213-219	7	4
β-strand	222-223	2	4
β-strand	229-230	2	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	257-263	7	4
β-strand	270-273	4	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	35-41	7	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	78-84	7	7
β-strand	91-94	4	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Chain G: 7 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	8
β-strand	17-19	3	9
β-strand	25-29	5	8
β-strand	34	1	8
β-strand	37-41	5	10
α-helix	50-52	3
β-strand	55	1	10
β-strand	59-60	2	8
α-helix	66-68	3
β-strand	70-76	7	10
β-strand	77	1	11
β-strand	85	1	11
β-strand	92-94	3	10
β-strand	95-97	3	9
β-strand	104-108	5	12
β-strand	112-114	3	13
β-strand	119-125	7	12
β-strand	131-136	6	14
α-helix	142-143	2
β-strand	144-147	4	14
β-strand	149-151	3	12
β-strand	154-161	8	12
α-helix	166-168	3
β-strand	170-178	9	14
β-strand	181-185	5	14
α-helix	186-191	6
β-strand	192-194	3	14
β-strand	195-197	3	13
α-helix	201-202	2
β-strand	204-207	4	15
β-strand	220-225	6	15
β-strand	231-236	6	13
β-strand	243-246	4	13
β-strand	248-250	3	15
β-strand	254-260	7	15
β-strand	270-276	7	13
β-strand	279-283	5	13
α-helix	284-289	6
β-strand	290	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	A0A411J078 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
NEF peptide	C	protein	8	Human immunodeficiency virus	P04601 (AlphaFold model)
Killer cell immunoglobulin-like receptor 3DL1	G	protein	305	Homo sapiens	P43629 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9BL9_1 MHC class I antigen (chains A)
GSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>9BL9_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>9BL9_3 NEF peptide (chains C)
RYPLTFGW

Sequence of entity 4 (G), FASTA

>9BL9_4 Killer cell immunoglobulin-like receptor 3DL1 (chains G)
HMGGQDKPFLSAWPSAVVPRGGHVTLRCHYRHRFNNFMLYKEDRIHVPIFHGRLFQESFN
MSPVTTAHAGNYTCRGSHPHSPTGWSAASNPVVIMVTGNHRKPSLLAHPGPLVKSGERVI
LQCWSDIMFEHFFLHKEGISKDPSRLVGQIHDGVSKANFSIGPMMFALAGTYRCYGSVTH
TPYQLSAPSDPLDIVVTGPYEKPSLSAQPGPKVQAGESVTLSCSSRSSYDMYHLSREGGA
HERRLPAVRKVNRTFQADFPLGPATHGGTYRCFGSFRHSPYEWSDPSDPLLVSVTGNPSH
HHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

An archaic HLA class I receptor allele diversifies natural killer cell-driven immunity in First Nations peoples of Oceania. Loh, L., Saunders, P.M., Faoro, C. et al. Cell (2024) 187:7008. DOI 10.1016/j.cell.2024.10.005 · PubMed

Other PDB entries of the same protein (UniProt A0A411J078 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BL5 2.0 Å, KIR3DL1*001 in complex with HLA-A*24:02 presenting the TW9 peptide
8RJI 2.3 Å, HLA A*2402-NF9_5R pMHC complex
9BL6 2.4 Å, KIR3DL1*114 in complex with HLA-A*24:02 presenting the TW9 peptide
8RJH 2.6 Å, HLA A*2402-NF9_6F pMHC complex
9BLA 3.0 Å, KIR3DL1*086 in complex with HLA-A*24:02 presenting the NEF peptide
28IL 3.1 Å, P1-15 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex

Browse structure collections

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