7KHF: LILRB1 D3D4 domain-inserted antibody MDB1 Fab

CryoEM structure of LILRB1 D3D4 domain-inserted antibody MDB1 Fab in complex with Plasmodium RIFIN (PF3D7_1373400) V2 domain. Determined by electron microscopy at 3.54 Å resolution. Released 31 Mar 2021.

Method: Electron microscopy
Resolution: 3.54 Å
Organisms: Homo sapiens, Plasmodium falciparum (isolate 3D7)
Chains: 6
Atoms: 11,559
Mol. weight: 171.49 kDa
Ligands: NAG
Released: 31 Mar 2021

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

Secondary structure: helices and β-sheets

7KHF contains 36 α-helices and 143 β-strands across 6 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, 43 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	23
β-strand	11-12	2	24
β-strand	20-25	6	23
β-strand	35-41	7	25
β-strand	48-54	7	25
β-strand	59-61	3	25
α-helix	63-65	3
β-strand	71-74	4	23
β-strand	79-82	4	23
β-strand	93-102	10	25
β-strand	110-115	6	25
β-strand	119-121	3	25
β-strand	122-123	2	24
β-strand	132-136	5	26
β-strand	140-141	2	27
β-strand	146-153	8	26
β-strand	159-164	6	28
β-strand	172-175	4	28
β-strand	179	1	29
β-strand	182	1	29
β-strand	183-191	9	26
α-helix	194-196	3
β-strand	198-205	8	28
α-helix	214-218	5
β-strand	219-221	3	28
β-strand	222-223	2	27
β-strand	231-235	5	30
β-strand	240-242	3	31
β-strand	246-253	8	30
β-strand	259-264	6	32
β-strand	272-275	4	32
β-strand	277-278	2	30
β-strand	283-291	9	30
β-strand	298-302	5	32
β-strand	305	1	32
β-strand	312	1	27
α-helix	315-319	5
β-strand	320-322	3	32
β-strand	323-325	3	31
β-strand	332-336	5	33
β-strand	347-357	11	33
β-strand	362-366	5	34
β-strand	376-377	2	33
α-helix	378-380	3
β-strand	381-382	2	33
β-strand	388-397	10	33
α-helix	398-403	6
β-strand	407-412	6	34
β-strand	417-422	6	34

Chain B: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	35
β-strand	10-12	3	36
β-strand	18-23	6	35
β-strand	33-37	5	37
β-strand	44-48	5	37
β-strand	52-53	2	37
β-strand	61-66	6	35
β-strand	69-74	6	35
β-strand	84-88	5	37
β-strand	89-90	2	38
β-strand	97-98	2	38
β-strand	103-104	2	37
β-strand	105-107	3	36
β-strand	113	1	39
β-strand	116-120	5	40
α-helix	121-123	3
β-strand	132-141	10	40
β-strand	142	1	39
β-strand	151-152	2	41
β-strand	155-156	2	41
β-strand	162-163	2	40
α-helix	164-166	3
β-strand	167	1	40
β-strand	174-182	9	40
α-helix	184-189	6
β-strand	193-199	7	41
β-strand	202-208	7	41

Chain C: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	188-204	17
α-helix	208-211	4
α-helix	213-216	4
α-helix	226-236	11
α-helix	239-241	3
β-strand	245	1	43
β-strand	254	1	43
α-helix	262-271	10
β-strand	276-277	2	9
α-helix	282-302	21

Chain D: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	188-204	17
α-helix	208-215	8
α-helix	227-236	10
α-helix	239-241	3
β-strand	245	1	42
β-strand	254	1	42
α-helix	262-271	10
α-helix	283-302	20

Chain H: 8 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	11-12	2	2
β-strand	18-22	5	3
β-strand	24-25	2	1
β-strand	34-40	7	4
β-strand	48-54	7	4
β-strand	59-61	3	4
α-helix	63-68	6
β-strand	71-74	4	3
β-strand	79-84	6	3
β-strand	93-94	2	5
β-strand	96-101	6	4
β-strand	102-104	3	6
β-strand	107-110	4	6
β-strand	120-121	2	5
β-strand	122-123	2	2
α-helix	130-131	2
β-strand	132-136	5	7
β-strand	140-141	2	8
β-strand	148-153	6	7
β-strand	159-164	6	9
β-strand	172-175	4	9
β-strand	183-185	3	7
β-strand	188	1	7
α-helix	194-196	3
β-strand	198-205	8	9
α-helix	214-218	5
β-strand	219-221	3	9
β-strand	222-224	3	8
β-strand	230	1	10
β-strand	231-235	5	11
β-strand	240-241	2	12
β-strand	247-253	7	11
β-strand	260-264	5	13
α-helix	270-271	2
β-strand	272-274	3	13
β-strand	277-279	3	11
β-strand	282-290	9	11
β-strand	298-303	6	13
β-strand	305	1	8
β-strand	312-313	2	8
β-strand	315	1	10
α-helix	316-319	4
β-strand	320-322	3	13
β-strand	323-324	2	12
α-helix	326-328	3
β-strand	333-336	4	14
β-strand	347	1	15
β-strand	350-357	8	14
β-strand	363-366	4	16
β-strand	375-382	8	14
β-strand	388-394	7	14
β-strand	397	1	15
β-strand	407-411	5	16
α-helix	413-415	3
β-strand	418-422	5	16

Chain L: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	17
β-strand	10-12	3	18
β-strand	18-23	6	17
α-helix	25-28	4
β-strand	33-37	5	19
β-strand	44-48	5	19
β-strand	53	1	19
β-strand	61-66	6	17
β-strand	69-74	6	17
β-strand	83	1	18
β-strand	84-90	7	19
β-strand	97-99	3	19
β-strand	105-107	3	18
α-helix	111-112	2
β-strand	113	1	20
β-strand	116-120	5	21
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	21
β-strand	142	1	20
β-strand	147-152	6	22
β-strand	155-156	2	22
β-strand	162-163	2	21
α-helix	164-166	3
β-strand	167	1	21
β-strand	174-182	9	21
α-helix	184-187	4
β-strand	193-198	6	22
β-strand	204-208	5	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MDB1 Fab heavy chain	A, H	protein	427	Homo sapiens
MDB1 Fab light chain	B, L	protein	214	Homo sapiens
Rifin	C, D	protein	151	Plasmodium falciparum (isolate 3D7)	C0H5N9 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>7KHF_1 MDB1 Fab heavy chain (chains A, H)
QITLKESGPTLVERTQTLTLTCTFSGFSLTTDGLGVGWIRQPPGKALEWLALIYYDDVRR
YRPSLKSRLTITKDTSKNRVVLTVTDMDPVDAGTYFCVHASLFNLGSRNVYFRYWGQGTL
VSVSSGVSKKPSLSVQPGPIVAPEETLTLQCGSDAGYNRFVLYKDGERDFLQLAGAQPQA
GLSQANFTLGPVSRSYGGQYRCYGAHNLSSEWSAPSDPLDILIAGQFYDRVSLSVQPGPT
VASGENVTLLCQSQGWMQTFLLTKEGAADDPWRLRSTYQSQKYQAEFPMGPVTSAHAGTY
RCYGSQSSKPYLLTHPSDPLELVVSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPE
PVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVD
KRVESKY

Sequence of entity 2 (B, L), FASTA

>7KHF_2 MDB1 Fab light chain (chains B, L)
SYDLTQPPSVSVSPGQTARITCSGDSLARQFASWYQQKPGQSPVLLIYKNIERLSAIPER
FSGSTSGTSVTLTISGVQAEDEADYFCQSADDSGSYSLFGTGTRVSVLGQPKANPTVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (C, D), FASTA

>7KHF_3 Rifin (chains C, D)
KELAEKAGALAGEAARIPAAIDAVIEGIKSKFSIDTLGGEALKSVIDGTNYYDASYITTA
IYNKFQVSSCLPSVPFLGGPPVPGAGANKPICSAVDKLYLGSGNFLDKSSLPGSIQKDVA
KIVAGAEQAAKAKAAMVASDKTLAVETAKKQ

Ligands and cofactors

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

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 C0H5N9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7KFK 2.63 Å, Crystal structure of LILRB1 D3D4 domain in complex with Plasmodium RIFIN (PF3D7_1373400)…

Browse structure collections

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