7KFK: LILRB1 D3D4 domain

Crystal structure of LILRB1 D3D4 domain in complex with Plasmodium RIFIN (PF3D7_1373400) V2 domain. Determined by X-ray diffraction at 2.63 Å resolution. Released 31 Mar 2021.

Method: X-ray diffraction
Resolution: 2.63 Å
Organisms: Homo sapiens, Plasmodium falciparum (isolate 3D7)
Chains: 4
Atoms: 5,150
Mol. weight: 83.37 kDa
Ligands: NAG
Released: 31 Mar 2021

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

Secondary structure: helices and β-sheets

7KFK contains 25 α-helices and 53 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: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	223-225	3
β-strand	227-231	5	1
β-strand	235-236	2	2
β-strand	243-248	6	1
β-strand	254-259	6	3
β-strand	267-270	4	3
β-strand	274	1	4
β-strand	277	1	4
β-strand	278-283	6	1
α-helix	289-291	3
β-strand	293-300	8	3
α-helix	306-307	2
α-helix	309-313	5
β-strand	314-316	3	3
β-strand	317-318	2	2
β-strand	326-330	5	5
β-strand	335-336	2	6
β-strand	341-348	8	5
β-strand	354-359	6	6
β-strand	367-370	4	6
β-strand	372-374	3	5
β-strand	377-386	10	5
α-helix	389-391	3
β-strand	393-400	8	6
β-strand	407	1	2
β-strand	408	1	6
α-helix	410-414	5
β-strand	415-420	6	6
β-strand	423-427	5	6

Chain B: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	223-225	3
β-strand	227-231	5	7
β-strand	235-236	2	8
β-strand	242-248	7	7
β-strand	254-259	6	9
β-strand	267-270	4	9
β-strand	274	1	10
β-strand	277	1	10
β-strand	278-284	7	7
α-helix	289-291	3
β-strand	293-300	8	9
α-helix	306-307	2
α-helix	309-313	5
β-strand	314-316	3	9
β-strand	317-318	2	8
β-strand	327-330	4	11
β-strand	335-336	2	12
α-helix	340	1
β-strand	341-348	8	11
β-strand	354-359	6	12
β-strand	367-370	4	12
β-strand	372-374	3	11
β-strand	377-386	10	11
α-helix	389-391	3
β-strand	393-400	8	12
β-strand	407	1	8
α-helix	410-414	5
β-strand	415-420	6	12
β-strand	423-427	5	12

Chain C: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	182-203	22
α-helix	208-214	7
α-helix	226-237	12
α-helix	239-242	4
β-strand	245	1	14
β-strand	254	1	14
α-helix	262-271	10
β-strand	274	1	9
β-strand	277-278	2	9
α-helix	282-311	30

Chain E: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	185-203	19
α-helix	208-218	11
α-helix	226-237	12
α-helix	239-242	4
β-strand	245	1	13
β-strand	254	1	13
α-helix	262-271	10
β-strand	274	1	3
β-strand	277-278	2	3
α-helix	282-307	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Leukocyte immunoglobulin-like receptor subfamily B member 1	A, B	protein	233	Homo sapiens	Q8NHL6 (AlphaFold model)
Rifin	C, E	protein	151	Plasmodium falciparum (isolate 3D7)	C0H5N9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7KFK_1 Isoform 2 of Leukocyte immunoglobulin-like receptor subfamily B member 1 (chains A, B)
VSKKPSLSVQPGPIVAPEETLTLQCGSDAGYNRFVLYKDGERDFLQLAGAQPQAGLSQAN
FTLGPVSRSYGGQYRCYGAHNLSSEWSAPSDPLDILIAGQFYDRVSLSVQPGPTVASGEN
VTLLCQSQGWMQTFLLTKEGAADDPWRLRSTYQSQKYQAEFPMGPVTSAHAGTYRCYGSQ
SSKPYLLTHPSDPLELVVSGGGGLEVLFQGPGGSAWSHPQFEKGGHHHHHHHH

Sequence of entity 2 (C, E), FASTA

>7KFK_2 Rifin (chains C, E)
KELAEKAGALAGEAARIPAAIDAVIEGIKSKFSIDTLGGEALKSVIDGTNYYDASYITTA
IYNKFQVSSCLPSVPFLGGPPVPGAGANKPICSAVDKLYLGSGNFLDKSSLPGSIQKDVA
KIVAGAEQAAKAKAAMVASDKTLAVETAKKQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural basis of malaria RIFIN binding by LILRB1-containing antibodies. Chen, Y., Xu, K., Piccoli, L. et al. Nature (2021) 592:639-643. DOI 10.1038/s41586-021-03378-6 · PubMed

Other PDB entries of the same protein (UniProt Q8NHL6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1UGN 1.8 Å, Crystal structure of LIR1.02, one of the alleles of LIR1
1G0X 2.1 Å, Crystal structure of the ligand binding domain of lir-1 (ILT2)
3D2U 2.21 Å, Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor
6EWO 2.3 Å, Crystal structure of non-phosphorylated form of RTF PHOSPHOPEPTIDE BOUND TO HLA-A2 in…
6EWA 2.39 Å, Crystal structure of HLA-A2 in complex with LILRB1
4LL9 2.69 Å, Crystal structure of D3D4 domain of the LILRB1 molecule
4NO0 2.7 Å, Crystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to HLA-A2 in…
1VDG 2.8 Å, Crystal structure of LIR1.01, one of the alleles of LIR1
1UFU 3.0 Å, Crystal structure of ligand binding domain of immunoglobulin-like transcript 2 (ILT2;…
6ZDX 3.0 Å, RIFIN variable region bound to LILRB1 ectodomain
6K60 3.15 Å, Structural and functional basis for HLA-G isoform recognition of immune checkpoint…
6EWC 3.2 Å, Crystal structure of non-phosphorylated form of RLS PHOSPHOPEPTIDE BOUND TO HLA-A2 in…

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