6V3J: KIR3DL1

KIR3DL1 in complex with HLA-B*57:03 presenting the peptide LSSPVTKSF. Determined by X-ray diffraction at 1.98 Å resolution. Released 20 May 2020.

Method: X-ray diffraction
Resolution: 1.98 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 5,847
Mol. weight: 78.3 kDa
Ligands: NAG
Released: 20 May 2020

Explore 6V3J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V3J contains 19 α-helices and 63 β-strands across 3 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	152-161	10
α-helix	163-174	12
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
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

Chain G: 8 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	8
β-strand	17-19	3	9
β-strand	24-29	6	8
β-strand	37-41	5	10
α-helix	49-52	4
β-strand	55	1	10
β-strand	59-61	3	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
α-helix	148	1
β-strand	149-151	3	12
β-strand	154-161	8	12
α-helix	166-168	3
β-strand	170-177	8	14
β-strand	184	1	9
α-helix	187-191	5
β-strand	192-194	3	14
β-strand	195-197	3	13
α-helix	201-202	2
β-strand	204-208	5	15
β-strand	212	1	16
β-strand	220-225	6	15
β-strand	231-236	6	17
β-strand	243-246	4	17
β-strand	248-249	2	15
β-strand	255-260	6	15
β-strand	268-275	8	17
β-strand	282-283	2	13
α-helix	284-289	6
β-strand	290-292	3	17
β-strand	293	1	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA-B alpha chain (B*5703GB)	A	protein	275	Homo sapiens	I3ZN84 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Peptide Leu-Ser-Ser-Pro-Val-Thr-Lys-Ser-Phe	C	protein	9	synthetic construct
Killer cell immunoglobulin-like receptor 3DL1	G	protein	299	Homo sapiens	P43629 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6V3J_1 HLA-B alpha chain (B*5703GB) (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRMAPRAPWIEQEGPEYW
DGETRNMKASAQTYRENLRIALRYYNQSEAGSHIIQVMYGCDVGPDGRLLRGHNQYAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>6V3J_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6V3J_3 Peptide Leu-Ser-Ser-Pro-Val-Thr-Lys-Ser-Phe (chains C)
LSSPVTKSF

Sequence of entity 4 (G), FASTA

>6V3J_4 Killer cell immunoglobulin-like receptor 3DL1 (chains G)
HMGGQDKPFLSAWPSAVVPRGGHVTLRCHYRHRFNNFMLYKEDRIHIPIFHGRIFQESFN
MSPVTTAHAGNYTCRGSHPHSPTGWSAPSNPVVIMVTGNHRKPSLLAHPGPLVKSGERVI
LQCWSDIMFEHFFLHKEGISKDPSRLVGQIHDGVSKANFSIGPMMLALAGTYRCYGSVTH
TPYQLSAPSDPLDIVVTGPYEKPSLSAQPGPKVQAGESVTLSCSSRSSYDMYHLSREGGA
HERRLPAVRKVNRTFQADFPLGPATHGGTYRCFGSFRHSPYEWSDPSDPLLVSVTGNPS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

The molecular basis of how buried human leukocyte antigen polymorphism modulates natural killer cell function. Saunders, P.M., MacLachlan, B.J., Pymm, P. et al. Proc Natl Acad Sci U S A (2020) 117:11636-11647. DOI 10.1073/pnas.1920570117 · PubMed

Other PDB entries of the same protein (UniProt I3ZN84 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6V2P 1.3 Å, HLA-B*57:03 presenting the peptide ASLNLPAVSW
6V2Q 1.6 Å, HLA-B*57:03 presenting the peptide LSSPVTKSF
9BL4 1.75 Å, KIR3DL1*086 in complex with HLA-B*57:03 presenting the AW10 peptide
5VVP 2.0 Å, HLA-B*57:03 presenting LSSPVTKSW
9BL3 2.0 Å, KIR3DL1*114 in complex with HLA-B*57:03 presenting the AW10 peptide
9BL2 2.1 Å, KIR3DL1*001 in complex with HLA-B*57:03 presenting the AW10 peptide

Browse structure collections

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