6ULF: 4498 Fab

Crystal structure of 4498 Fab in complex with circumsporozoite protein NDN3 and anti-Kappa VHH domain. Determined by X-ray diffraction at 1.7 Å resolution. Released 17 Jun 2020.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Homo sapiens, Camelidae mixed library, Plasmodium falciparum
Chains: 4
Atoms: 4,802
Mol. weight: 60.68 kDa
Released: 17 Jun 2020

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

Secondary structure: helices and β-sheets

6ULF contains 22 α-helices and 56 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: 11 helices, 24 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	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	102-103	2	3
β-strand	109-110	2	3
β-strand	114-117	4	2
β-strand	121-125	5	2
α-helix	128-130	3
β-strand	131	1	4
α-helix	132-133	2
β-strand	134-138	5	5
α-helix	142-144	3
β-strand	145-146	2	5
β-strand	149-159	11	5
β-strand	160	1	4
β-strand	165-168	4	6
α-helix	169-171	3
β-strand	177-179	3	5
α-helix	180-182	3
β-strand	183-184	2	5
β-strand	190-199	10	5
α-helix	200-203	4
β-strand	209-214	6	6
α-helix	215-217	3
β-strand	219-224	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	96-97	2	8
β-strand	101-105	5	8
β-strand	110	1	9
α-helix	111-112	2
β-strand	113-117	5	10
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	10
β-strand	139	1	9
β-strand	143-149	7	11
β-strand	152-153	2	11
α-helix	154	1
β-strand	158-162	5	10
α-helix	163-166	4
β-strand	172-181	10	10
α-helix	182-185	4
β-strand	190-197	8	11
β-strand	204-209	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
β-strand	46-51	6	13
β-strand	58-60	3	13
α-helix	62-64	3
β-strand	68-73	6	12
α-helix	74-76	3
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-99	8	13
β-strand	108-111	4	13
β-strand	115-119	5	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
4498 Fab heavy chain	A	protein	230	Homo sapiens
4498 Fab light chain	B	protein	213	Homo sapiens
anti Kappa VHH domain	K	protein	121	Camelidae mixed library
Circumsporozoite protein	P	protein	12	Plasmodium falciparum	P19597 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6ULF_1 4498 Fab heavy chain (chains A)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSIYGMHWVRQAPGKGLEWVALIWYDGTNKYY
TDSVKGRFTISRDNSKNTLFLQMNSVRAEDTAVYYCARDAHYSDSSGYSSWGYFDYWGQG
SLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (B), FASTA

>6ULF_2 4498 Fab light chain (chains B)
EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIFDASIRATGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWYTFGQGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (K), FASTA

>6ULF_3 anti Kappa VHH domain (chains K)
XVQLXXSGGGXVQXGXSLXLSCXAXXXXXXXXXXXWXRQXPGXXREXVXXXXXXXXXXXX
XDSXXGRFTXSXDXXXXXXXLQXXXLXXXDXAXYYCXXXXXXXXXXXXXXWGXGTXVTVS
S

Sequence of entity 4 (P), FASTA

>6ULF_4 Circumsporozoite protein (chains P)
NANPNVDPNANP

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:

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…
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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