7RXL: Fab1488

Fab1488 in complex with the C-terminal alpha-TSR domain of P. falciparum. Determined by X-ray diffraction at 1.82 Å resolution. Released 16 Mar 2022.

Method: X-ray diffraction
Resolution: 1.82 Å
Organisms: Homo sapiens, Plasmodium falciparum (isolate 3D7)
Chains: 6
Atoms: 7,652
Mol. weight: 107.72 kDa
Released: 16 Mar 2022

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

Secondary structure: helices and β-sheets

7RXL contains 47 α-helices and 96 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 C: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	10-12	3	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	20
β-strand	45-51	7	20
β-strand	57-59	3	20
β-strand	67-72	6	19
α-helix	73-75	3
β-strand	77-82	6	19
α-helix	84-86	3
β-strand	88-96	9	20
β-strand	100C-103	5	20
β-strand	107-111	5	20
α-helix	115-116	2
β-strand	117	1	21
α-helix	118-119	2
β-strand	120-124	5	22
α-helix	128-130	3
β-strand	131-132	2	22
β-strand	135-145	11	22
β-strand	146	1	21
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-165	3	22
α-helix	166-168	3
β-strand	169-170	2	22
β-strand	176-185	10	22
α-helix	186-188	3
β-strand	195-200	6	6
α-helix	201-203	3
β-strand	205-210	6	6

Chain D: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	13
β-strand	9-13	4	14
α-helix	18	1
β-strand	19-24	6	13
α-helix	28-30	3
β-strand	34-38	5	14
β-strand	45-48	4	14
β-strand	49	1	15
β-strand	53	1	15
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	84-92	9	14
β-strand	95-98	4	14
β-strand	102-106	5	14
α-helix	108-110	3
β-strand	111	1	16
α-helix	112-113	2
β-strand	114-118	5	17
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	17
β-strand	140	1	16
β-strand	145-150	6	18
β-strand	153-155	3	18
β-strand	159-161	3	17
α-helix	162-164	3
β-strand	165-166	2	17
β-strand	172-180	9	17
α-helix	182-187	6
β-strand	191-197	7	18
β-strand	200-206	7	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	313-322	10
α-helix	331-334	4
β-strand	338-346	9	23
α-helix	348-350	3
α-helix	355-357	3
α-helix	360-363	4
β-strand	364-372	9	23

Chain F: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	313-322	10
α-helix	324-326	3
α-helix	331-334	4
β-strand	340-346	7	24
α-helix	348-350	3
α-helix	355-357	3
α-helix	360-363	4
β-strand	364-370	7	24
α-helix	373-374	2

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	45-51	7	9
β-strand	57-59	3	9
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-96	9	9
β-strand	100C-103	5	9
β-strand	107-109	3	9
β-strand	110-111	2	8
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
β-strand	132	1	11
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-154	4	12
α-helix	155-157	3
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-170	2	11
β-strand	176-185	10	11
α-helix	186-188	3
β-strand	195-200	6	12
α-helix	201-203	3
β-strand	205-210	6	12

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	9-13	4	2
α-helix	18	1
β-strand	19-24	6	1
α-helix	28-30	3
β-strand	34-38	5	2
β-strand	45-48	4	2
β-strand	49	1	3
β-strand	53	1	3
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-92	9	2
β-strand	95-98	4	2
β-strand	102-106	5	2
α-helix	108-110	3
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	122-126	5
β-strand	130-139	10	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-155	3	6
β-strand	159-161	3	5
α-helix	162-164	3
β-strand	165-166	2	5
β-strand	172-180	9	5
α-helix	182-187	6
β-strand	191-197	7	6
β-strand	200-206	7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab1488 light chain	D, L	protein	212	Homo sapiens
Fab1488 heavy chain	C, H	protein	224	Homo sapiens
Circumsporozoite protein	E, F	protein	66	Plasmodium falciparum (isolate 3D7)	Q7K740 (AlphaFold model)

Sequence of entity 1 (D, L), FASTA

>7RXL_1 Fab1488 light chain (chains D, L)
SYELTQPPSVSVSPGQTASITCSGDKLGDKFACWYQQKPGQSPVLVIYQDTKRPSGIPER
FSGSNSGNTATLTISGTQAMDEADYYCQAWDSSTVVFGGGTKVTVLGQPKAAPSVTLFPP
SSEELQANKATLVCLVSDFYPGAVTVAWKADGSPVKVGVETTKPSKQSNNKYAASSYLSL
TPEQWKSHRSYSCRVTHEGSTVEKTVAPAECS

Sequence of entity 2 (C, H), FASTA

>7RXL_2 Fab1488 heavy chain (chains C, H)
EVHLVESGGGLVKPGGSLRLSCAASGFTFSSYTMNWVRQAPGKGLEWVSSISSSSTYIYY
ADSVRGRFTISRDNAKNSLYLQMNSLRAEDSAVYYCARRAGGFDAYYFDYWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (E, F), FASTA

>7RXL_3 Circumsporozoite protein (chains E, F)
EPSDKHIKEYLNKIQNSLSTEWSPCSVTCGNGIQVRIKPGSANKPKDELDYANDIEKKIC
KMEKCS

Primary citation

A novel CSP C-terminal epitope targeted by an antibody with protective activity against Plasmodium falciparum. Beutler, N., Pholcharee, T., Oyen, D. et al. PLoS Pathog (2022) 18:e1010409-e1010409. DOI 10.1371/journal.ppat.1010409 · PubMed

Other PDB entries of the same protein (UniProt Q7K740 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SG5 1.4 Å, Structure of PfCSP peptide 21 with antibody CIS43_Var2
9C79 1.46 Å, Human monoclonal antibody MAD21-101 bound to the N-terminus of cleaved circumsporozoite…
9NKZ 1.48 Å, Crystal structure of Fab MAM01 in complex with NANP6 peptide from circumsporozoite protein
9NL0 1.54 Å, Crystal structure of Fab MAM01 in complex with NPNA3 peptide from circumsporozoite protein
7SG6 1.55 Å, Structure of PfCSP peptide 21 with antibody CIS43_Var10
6PBV 1.57 Å, Crystal structure of Fab668 complex
9NCY 1.63 Å, Fab1392 in complex with the C-terminal alpha-TSR domain of the P. falciparum…
3VDJ 1.7 Å, Crystal structure of circumsporozoite protein aTSR domain, R32 native form
9DST 1.74 Å, Crystal structure of Fab MS-1805 in complex with N-terminal junction peptide from…
9NI1 1.75 Å, Fab389 in complex with the C-terminal alpha-TSR domain of the P. falciparum…
7RXP 1.76 Å, Fab1512 in complex with the C-terminal alpha-TSR domain of P. falciparum
6BQB 1.77 Å, MGG4 Fab in complex with peptide

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