8F9V: Ky15.8 Fab

Crystal structure of Ky15.8 Fab in complex with circumsporozoite protein KQPA peptide. Determined by X-ray diffraction at 2.25 Å resolution. Released 1 Nov 2023.

Method: X-ray diffraction
Resolution: 2.25 Å
Organisms: Mus musculus, Plasmodium falciparum (isolate NF54)
Chains: 12
Atoms: 14,579
Mol. weight: 198.61 kDa
Released: 1 Nov 2023

Explore 8F9V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F9V contains 74 α-helices and 180 β-strands across 8 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 C: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-40	7	3
β-strand	44-51	8	3
β-strand	57-59	3	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	3
α-helix	96	1
β-strand	100E-103	4	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	114-116	3
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
α-helix	128-130	3
β-strand	131-132	2	5
β-strand	135-145	11	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-185	10	5
α-helix	186-188	3
β-strand	195-200	6	6
α-helix	201-203	3
β-strand	205-210	6	6
α-helix	212-214	3

Chain B: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	3
β-strand	18-25	8	7
β-strand	33-38	6	3
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-76	7	7
α-helix	80-82	3
β-strand	85-90	6	3
β-strand	97-98	2	3
β-strand	102-106	5	3
β-strand	111	1	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	144-150	7	10
β-strand	153-154	2	10
α-helix	155	1
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-187	5
β-strand	191-198	8	10
β-strand	205-210	6	10

Chain D: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	13
β-strand	18-25	8	17
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	17
β-strand	70-76	7	17
α-helix	80-82	3
β-strand	85-90	6	13
β-strand	97-98	2	13
β-strand	102-106	5	13
β-strand	111	1	18
α-helix	112-113	2
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	19
β-strand	140	1	18
β-strand	145-150	6	20
β-strand	153-154	2	20
α-helix	155	1
β-strand	159-163	5	19
α-helix	164-167	4
β-strand	173-182	10	19
α-helix	183-187	5
β-strand	191-197	7	20
β-strand	205-210	6	20

Chains E and G: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	11-12	2	22
β-strand	18-25	8	21
α-helix	29-31	3
β-strand	34-40	7	23
β-strand	44-51	8	23
β-strand	57-59	3	23
β-strand	67-72	6	21
β-strand	77-82	6	21
α-helix	84-86	3
β-strand	88-95	8	23
α-helix	96	1
β-strand	100E-103	4	23
β-strand	107-109	3	23
β-strand	110-111	2	22
α-helix	114-116	3
β-strand	117	1	24
α-helix	118-119	2
β-strand	120-124	5	25
β-strand	131-132	2	25
β-strand	135-145	11	25
β-strand	146	1	24
β-strand	151-154	4	26
α-helix	155-157	3
β-strand	159	1	26
β-strand	163-165	3	25
α-helix	166-168	3
β-strand	169-170	2	25
β-strand	176-185	10	25
α-helix	186-188	3
β-strand	195-200	6	26
α-helix	201-203	3
β-strand	205-210	6	26
α-helix	212-215	4

Chains F and H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	27
β-strand	10-13	4	23
β-strand	18-25	8	27
β-strand	33-38	6	23
β-strand	45-49	5	23
β-strand	53-54	2	23
α-helix	55	1
β-strand	62-67	6	27
β-strand	70-76	7	27
α-helix	80-82	3
β-strand	85-90	6	23
β-strand	97-98	2	23
β-strand	102-106	5	23
β-strand	111	1	28
α-helix	112-113	2
β-strand	114-118	5	29
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	29
β-strand	140	1	28
β-strand	145-150	6	30
β-strand	153-154	2	30
α-helix	155	1
β-strand	159-163	5	29
α-helix	164-167	4
β-strand	173-182	10	29
α-helix	183-187	5
β-strand	191-197	7	30
β-strand	205-210	6	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ky15.8 Antibody, heavy chain	A, C, E, G	protein	225	Mus musculus
Ky15.8 Antibody, light chain	B, D, F, H	protein	213	Mus musculus
Circumsporozoite protein KQPA peptide	M, N, O, P	protein	15	Plasmodium falciparum (isolate NF54)	P19597 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>8F9V_1 Ky15.8 Antibody, heavy chain (chains A, C, E, G)
QVQLVESGGNVVQPGRSLRLSCTASGFTFSSYGMHWVRQAPDKGLEWVAIIWYDGGNKFY
ADSVKGRFTISRDNSKDTLYLQMNSLRAEDTAVYYCAKAWYKIDDKYSMDVWGQGTTVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (B, D, F, H), FASTA

>8F9V_2 Ky15.8 Antibody, light chain (chains B, D, F, H)
DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPS
RFSGSGSGTEFTLTISGLQPDDFATYYCQQYNSYWTFGQGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (M, N, O, P), FASTA

>8F9V_3 Circumsporozoite protein KQPA peptide (chains M, N, O, P)
KQPADGNPDPNANPN

Primary citation

Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein. Thai, E., Murugan, R., Binter, S. et al. Cell Rep (2023) 42:113330-113330. DOI 10.1016/j.celrep.2023.113330 · PubMed

Other PDB entries of the same protein (UniProt P19597 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6O24 1.4 Å, Crystal structure of 4498 Fab in complex with circumsporozoite protein NANP3 and…
8FDD 1.54 Å, Crystal structure of Ky15.3 Fab in complex with circumsporozoite protein NPDP peptide
8FAS 1.55 Å, Crystal structure of Ky230 Fab in complex with circumsporozoite protein NANP5 peptide
6VLN 1.63 Å, Crystal structure of 4498 Fab in complex with circumsporozoite protein DND3 and…
8FB8 1.69 Å, Crystal structure of Ky15.10-Y100EK Fab in complex with circumsporozoite protein KQPA…
6ULF 1.7 Å, Crystal structure of 4498 Fab in complex with circumsporozoite protein NDN3 and…
8F9U 1.7 Å, Crystal structure of Ky15.7 Fab in complex with circumsporozoite protein NPDP peptide
8FB7 1.75 Å, Crystal structure of Ky15.10 Fab in complex with circumsporozoite protein NPDP peptide
6O26 1.8 Å, Crystal structure of 3246 Fab in complex with circumsporozoite protein NANA
8FA7 1.8 Å, Crystal structure of Ky15.11 Fab in complex with circumsporozoite protein KQPA peptide
8FA8 1.8 Å, Crystal structure of Ky15.11 Fab in complex with circumsporozoite protein NDN peptide
8FDC 1.8 Å, Crystal structure of Ky311 Fab in complex with circumsporozoite protein KQPA peptide

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