7K80: KIR3DL1*001

KIR3DL1*001 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide. Determined by X-ray diffraction at 2.4 Å resolution. Released 9 Dec 2020.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, synthetic construct
Chains: 8
Atoms: 11,001
Mol. weight: 157 kDa
Ligands: NAG
Released: 9 Dec 2020

Explore 7K80 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7K80 contains 41 α-helices and 126 β-strands across 7 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.

Chains A and D: 10 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	57-84	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	152-159	8
α-helix	160-164	5
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	214-219	6	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	257-262	6	4
β-strand	270-273	4	4

Chains B and E: 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 F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Chain G: 8 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	15
β-strand	17-19	3	16
β-strand	24-29	6	15
β-strand	30	1	17
β-strand	34	1	17
β-strand	37-41	5	18
α-helix	49-52	4
α-helix	53-54	2
β-strand	55	1	18
β-strand	59-61	3	15
α-helix	66-68	3
β-strand	70-76	7	18
β-strand	77	1	19
β-strand	85	1	19
β-strand	92-94	3	18
β-strand	95-97	3	16
β-strand	104-108	5	20
β-strand	112-114	3	21
β-strand	119-125	7	20
β-strand	131-136	6	22
α-helix	142-143	2
β-strand	144-147	4	22
β-strand	149-151	3	20
β-strand	154-161	8	20
α-helix	166-168	3
β-strand	170-177	8	22
β-strand	184	1	16
α-helix	186-191	6
β-strand	192-194	3	22
β-strand	195-197	3	21
α-helix	201-203	3
β-strand	204-208	5	23
β-strand	212-213	2	24
β-strand	218-225	8	23
β-strand	231-236	6	21
β-strand	242-246	5	21
β-strand	248-249	2	23
β-strand	255-263	9	23
β-strand	269-276	8	21
β-strand	279-283	5	21
α-helix	285-289	5
β-strand	290-291	2	21
β-strand	293-294	2	24

Chain H: 8 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	25
β-strand	17-19	3	26
β-strand	24-29	6	25
β-strand	37-41	5	27
α-helix	49-51	3
α-helix	53-54	2
β-strand	55	1	27
α-helix	56	1
β-strand	59-61	3	25
β-strand	70-76	7	27
β-strand	77	1	28
β-strand	85	1	28
β-strand	92-94	3	27
β-strand	95-97	3	26
β-strand	104-108	5	29
β-strand	112-114	3	30
β-strand	119-125	7	29
β-strand	131-136	6	31
α-helix	142-143	2
β-strand	144-147	4	31
β-strand	149-151	3	29
β-strand	154-161	8	29
α-helix	166-168	3
β-strand	170-177	8	31
β-strand	184	1	26
α-helix	186-191	6
β-strand	192-194	3	31
β-strand	195-197	3	30
α-helix	201-202	2
β-strand	204-207	4	32
β-strand	220-225	6	32
β-strand	231-236	6	30
β-strand	243-246	4	30
β-strand	248-250	3	32
β-strand	254-260	7	32
β-strand	268-276	9	30
β-strand	279-283	5	30
α-helix	284-289	6
β-strand	290-292	3	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, D	protein	276	Homo sapiens	A0A5H2UYS3 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	100	Homo sapiens	P61769 (AlphaFold model)
Arg-tyr-pro-leu-thr-phe-gly-trp	C, F	protein	8	synthetic construct	P04601 (AlphaFold model)
Killer cell immunoglobulin-like receptor 3DL1	G, H	protein	299	Homo sapiens	P43629 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>7K80_1 MHC class I antigen (chains A, D)
GSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, E), FASTA

>7K80_2 Beta-2-microglobulin (chains B, E)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F), FASTA

>7K80_3 ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP (chains C, F)
RYPLTFGW

Sequence of entity 4 (G, H), FASTA

>7K80_4 Killer cell immunoglobulin-like receptor 3DL1 (chains G, H)
HMGGQDKPFLSAWPSAVVPRGGHVTLRCHYRHRFNNFMLYKEDRIHIPIFHGRIFQESFN
MSPVTTAHAGNYTCRGSHPHSPTGWSAPSNPVVIMVTGNHRKPSLLAHPGPLVKSGERVI
LQCWSDIMFEHFFLHKEGISKDPSRLVGQIHDGVSKANFSIGPMMLALAGTYRCYGSVTH
TPYQLSAPSDPLDIVVTGPYEKPSLSAQPGPKVQAGESVTLSCSSRSSYDMYHLSREGGA
HERRLPAVRKVNRTFQADFPLGPATHGGTYRCFGSFRHSPYEWSDPSDPLLVSVTGNPS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Water and common crystallization additives (ACT, FMT) are not listed.

Primary citation

The Role of the HLA Class I alpha 2 Helix in Determining Ligand Hierarchy for the Killer Cell Ig-like Receptor 3DL1. Saunders, P.M., MacLachlan, B.J., Widjaja, J. et al. J Immunol (2021) 206:849-860. DOI 10.4049/jimmunol.2001109 · PubMed

Other PDB entries of the same protein (UniProt A0A5H2UYS3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7JYV 1.51 Å, Crystal Structure of HLA A*2402 in complex with YFSPIRVTF, an 9-mer influenza epitope
7MJA 1.69 Å, HLA-A*24:02 bound to Neuroblastoma derived PHOX2B peptide
7EJM 1.71 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-229E) spike protein
8SBK 1.8 Å, Structure of HLA-A*24:02 in complex with peptide, LYLPVRVLI (ATG2A).
7WT3 1.89 Å, Crystal structure of HLA-A*2402 complexed with 4-mer lipopeptide
7EJL 1.89 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-2) spike protein
7WT4 1.89 Å, Crystal structure of HLA-A*2402 complexed with 8-mer Influenza PB1 peptide
7K81 2.0 Å, KIR3DL1*005 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide
7EJN 2.11 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-HKU1) spike protein
6XQA 2.16 Å, Crystal Structure of HLA A*2402 in complex with TYQWVLKNL, an 9-mer epitope from…
7NME 2.2 Å, Human MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR
7NMD 2.25 Å, Human Major Histocompatibility Complex A24 Allele presenting QLPRLFPLL

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