9F2D: KIR2DL1

KIR2DL1 bound to RIFIN RBK21. Determined by X-ray diffraction at 2.89 Å resolution. Released 9 Apr 2025.

Method: X-ray diffraction
Resolution: 2.89 Å
Organisms: Plasmodium falciparum, Homo sapiens
Chains: 16
Atoms: 18,222
Mol. weight: 302.34 kDa
Ligands: NAG
Released: 9 Apr 2025

Explore 9F2D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F2D contains 93 α-helices and 181 β-strands across 16 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: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	166-185	20
α-helix	193-196	4
α-helix	207-218	12
α-helix	220-225	6
β-strand	228	1	1
β-strand	231	1	1
α-helix	235-238	4
α-helix	239-243	5
β-strand	257-258	2	2
α-helix	259-273	15

Chain B: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	30-34	5	3
β-strand	38-40	3	4
β-strand	45-51	7	3
β-strand	57-64	8	2
β-strand	68-73	6	2
α-helix	74	1
β-strand	75-77	3	3
β-strand	80-87	8	3
α-helix	92-94	3
β-strand	96-103	8	2
β-strand	104	1	5
β-strand	107	1	5
α-helix	113-117	5
β-strand	118-120	3	2
β-strand	121-123	3	4
α-helix	127-129	3
β-strand	130-134	5	6
β-strand	138	1	7
β-strand	144-151	8	6
β-strand	157-162	6	8
β-strand	169-171	3	8
β-strand	176-177	2	6
β-strand	180-189	10	6
β-strand	194-202	9	8
β-strand	205-209	5	8
α-helix	211-215	5
β-strand	216-218	3	8
β-strand	219	1	7

Chain C: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	168-184	17
α-helix	193-198	6
α-helix	207-218	12
α-helix	220-224	5
α-helix	235-238	4
α-helix	239-243	5
β-strand	257-258	2	9
α-helix	259-272	14

Chain D: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	30-34	5	10
β-strand	38-40	3	11
β-strand	45-51	7	10
β-strand	57-63	7	9
β-strand	69-72	4	9
β-strand	75-77	3	10
β-strand	80-87	8	10
α-helix	92-94	3
β-strand	96-105	10	9
β-strand	110-111	2	9
α-helix	113-117	5
β-strand	118-120	3	9
β-strand	121-123	3	11
β-strand	130-134	5	12
β-strand	138-139	2	13
β-strand	144-151	8	12
β-strand	157-162	6	14
β-strand	169-172	4	14
β-strand	174-175	2	12
β-strand	181-189	9	12
β-strand	194-202	9	14
β-strand	205-209	5	14
α-helix	211-215	5
β-strand	216-218	3	14
β-strand	219-220	2	13

Chains E and I: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	167-185	19
α-helix	193-196	4
α-helix	207-218	12
α-helix	220-225	6
α-helix	235-238	4
α-helix	239-243	5
β-strand	257-258	2	15
α-helix	259-272	14

Chain F: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	30-34	5	16
β-strand	38-40	3	17
β-strand	45-51	7	16
β-strand	57-63	7	15
β-strand	68-73	6	15
α-helix	74	1
β-strand	75-76	2	16
β-strand	81-87	7	16
α-helix	92-94	3
β-strand	96-103	8	15
α-helix	113-117	5
β-strand	118-120	3	15
β-strand	121-123	3	17
β-strand	130-134	5	18
β-strand	138-139	2	19
β-strand	144-151	8	18
β-strand	157-162	6	20
α-helix	168	1
β-strand	169-172	4	20
α-helix	177-179	3
β-strand	181-189	9	18
β-strand	194-202	9	20
β-strand	205-209	5	20
α-helix	210-215	6
β-strand	216-218	3	20
β-strand	219-220	2	19

Chain G: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	167-185	19
α-helix	196-198	3
α-helix	208-218	11
α-helix	220-223	4
α-helix	235-238	4
α-helix	239-243	5
β-strand	257-258	2	21
α-helix	259-272	14

Chain H: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	30-34	5	22
β-strand	38-40	3	23
β-strand	45-51	7	22
β-strand	58-64	7	21
β-strand	68-72	5	21
β-strand	75-77	3	22
β-strand	80-87	8	22
α-helix	92-94	3
β-strand	96-101	6	21
α-helix	112-117	6
β-strand	118-120	3	21
β-strand	121-123	3	23
β-strand	130-134	5	24
β-strand	138-139	2	25
β-strand	144-151	8	24
β-strand	157-162	6	26
α-helix	168	1
β-strand	169-171	3	26
β-strand	176	1	24
β-strand	181-189	9	24
β-strand	194-202	9	26
β-strand	205-209	5	26
α-helix	211-215	5
β-strand	216-218	3	26
β-strand	219-220	2	25

7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rifin RBK21	A, C, E, G, I, K, M, O	protein	152	Plasmodium falciparum	W7F7W4 (AlphaFold model)
KIR2DL protein	B, D, F, H, J, L, N, P	protein	195	Homo sapiens	P43626 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K, M, O), FASTA

>9F2D_1 RIFIN RBK21 (chains A, C, E, G, I, K, M, O)
VALAKAIAEGAAKGAEVGEAARIAAAIDAVIKGIETKFGVSTNGVLGLKSLFTANNYNNA
TKIAGAIIEEYKPSSCLTGGSGADNSICPWAMENFFAARKIPGFIQREAVSMNDVIEKTV
KTIVSDAPKTAETAAKKATEEAIKASTDAVES

Sequence of entity 2 (B, D, F, H, J, L, N, P), FASTA

>9F2D_2 KIR2DL protein (chains B, D, F, H, J, L, N, P)
RKPSLLAHPGPLVKSEETVILQCWSDVMFEHFLLHREGMFNDTLRLIGEHHDGVSKANFS
ISRMTQDLAGTYRCYGSVTHSPYQVSAPSDPLDIVIIGLYEKPSLSAQPGPTVLAGENVT
LSCSSRSSYDMYHLSREGEAHERRLPAGPKVNGTFQADFPLGPATHGGTYRCFGSFHDSP
YEWSKSSDPLLVSVT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	15

Primary citation

RIFINs displayed on malaria-infected erythrocytes bind KIR2DL1 and KIR2DS1. Sakoguchi, A., Chamberlain, S.G., Morch, A.M. et al. Nature (2025) 643:1363-1371. DOI 10.1038/s41586-025-09091-y · PubMed

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