6O24: 4498 Fab

Crystal structure of 4498 Fab in complex with circumsporozoite protein NANP3 and anti-Kappa VHH domain. Determined by X-ray diffraction at 1.4 Å resolution. Released 1 Jul 2020.

Method: X-ray diffraction
Resolution: 1.4 Å
Organisms: Homo sapiens, Lama glama, Plasmodium falciparum
Chains: 4
Atoms: 4,900
Mol. weight: 61.11 kDa
Ligands: CIT
Released: 1 Jul 2020

Explore 6O24 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O24 contains 21 α-helices and 58 β-strands across 3 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: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	57-59	3	2
β-strand	64	1	1
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	98-99	2	3
β-strand	100E-100F	2	3
β-strand	100J-103	4	2
β-strand	107-111	5	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

Chain B: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
α-helix	155	1
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-197	7	11
β-strand	205-210	6	11

Chain K: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	10-12	3	13
β-strand	18-25	8	12
β-strand	34-39	6	13
α-helix	44-45	2
β-strand	46-51	6	13
β-strand	57-59	3	13
β-strand	67-72	6	12
α-helix	73-75	3
β-strand	77-82	6	12
α-helix	84-86	3
β-strand	88-95	8	13
β-strand	100D-103	4	13
β-strand	107-111	5	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
4498 Fab heavy chain	A	protein	230	Homo sapiens
4498 Kappa light chain	B	protein	213	Homo sapiens
Anti-kappa VHH domain	K	protein	121	Lama glama
Circumsporozoite protein	I	protein	12	Plasmodium falciparum	P19597 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6O24_1 4498 Fab heavy chain (chains A)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSIYGMHWVRQAPGKGLEWVALIWYDGTNKYY
TDSVKGRFTISRDNSKNTLFLQMNSVRAEDTAVYYCARDAHYSDSSGYSSWGYFDYWGQG
SLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 2 (B), FASTA

>6O24_2 4498 Kappa light chain (chains B)
EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIFDASIRATGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWYTFGQGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (K), FASTA

>6O24_3 Anti-kappa VHH domain (chains K)
XVQLXXSGGGXVQXGXSLXLSCXAXXXXXXXXXXXWXRQXPGXXREXVXXXXXXXXXXXX
XDSXXGRFTXSXDXXXXXXXLQXXXLXXXDXAXYYCXXXXXXXXXXXXXXWGXGTXVTVS
S

Sequence of entity 4 (I), FASTA

>6O24_4 Circumsporozoite protein (chains I)
NANPNANPNANP

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1

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

Primary citation

Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs. Murugan, R., Scally, S.W., Costa, G. et al. Nat Med (2020) 26:1135-1145. DOI 10.1038/s41591-020-0881-9 · PubMed

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

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
8F9T 1.85 Å, Crystal structure of Ky15.2 Fab in complex with circumsporozoite protein NPDP peptide

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