7RD3: Antibody m42.126 heavy chain

Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody m42.126. Determined by X-ray diffraction at 1.81 Å resolution. Released 15 Dec 2021.

Method: X-ray diffraction
Resolution: 1.81 Å
Organisms: Mus musculus, Plasmodium falciparum
Chains: 6
Atoms: 7,403
Mol. weight: 106.49 kDa
Released: 15 Dec 2021

Explore 7RD3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RD3 contains 37 α-helices and 93 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: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	46-52	7	2
β-strand	57-59	3	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-98	11	2
β-strand	100C-103	5	2
α-helix	104-106	3
β-strand	107-111	5	2
α-helix	115-116	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	187-189	3
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	2
β-strand	19-25	7	6
β-strand	27C-27D	2	7
β-strand	30-31	2	7
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
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	183-186	4
β-strand	191-198	8	10
β-strand	205-210	6	10

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	10	1	2

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
α-helix	7-9	3
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-52	8	12
β-strand	57-59	3	12
β-strand	67-72	6	11
β-strand	77-82	6	11
α-helix	84-86	3
β-strand	88-98	11	12
β-strand	100C-103	5	12
β-strand	107-111	5	12
α-helix	114-116	3
β-strand	117	1	13
α-helix	118-119	2
β-strand	120-124	5	14
α-helix	128-130	3
β-strand	131-132	2	14
β-strand	135-145	11	14
β-strand	146	1	13
β-strand	151-154	4	15
α-helix	155-157	3
β-strand	159	1	15
β-strand	163-165	3	14
α-helix	166-168	3
β-strand	169-170	2	14
β-strand	176-185	10	14
α-helix	186-188	3
β-strand	195-200	6	15
α-helix	201-203	3
β-strand	205-210	6	15

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-14	5	17
β-strand	19-25	7	16
β-strand	27C-27D	2	18
β-strand	30-31	2	18
β-strand	33-38	6	17
β-strand	45-49	5	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-90	7	17
α-helix	96	1
β-strand	97-98	2	17
β-strand	102-107	6	17
β-strand	111	1	19
α-helix	112-113	2
β-strand	114-118	5	20
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	20
β-strand	140	1	19
β-strand	144-150	7	21
β-strand	153-154	2	21
β-strand	159-163	5	20
α-helix	164-167	4
β-strand	173-182	10	20
α-helix	183-186	4
β-strand	191-198	8	21
β-strand	205-210	6	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
antibody m42.126 heavy chain	A, H	protein	255	Mus musculus
antibody m42.126 light chain	B, L	protein	220	Mus musculus
Circumsporozoite protein	C, D	protein	15	Plasmodium falciparum	P02893 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>7RD3_1 antibody m42.126 heavy chain (chains A, H)
QVQLVQSEAEVKKPGASVKVSCKASGYTFTRYAMHWVRQAPGQRLEWMGWIKAGNGDTRY
SQKFQGRVTITRDTSASTVYMEMSSLRSEDTAVYYCALLTVITSDDAFDIWGQGTMVTVS
LASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQGPGGSAW
SHPQFEKGGHHHHHH

Sequence of entity 2 (B, L), FASTA

>7RD3_2 antibody m42.126 light chain (chains B, L)
DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLVYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCHQYYSSPLTFGGGTKVEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, D), FASTA

>7RD3_3 Circumsporozoite protein (chains C, D)
NPDPNANPNVDPNAN

Primary citation

Vaccination in a humanized mouse model elicits highly protective PfCSP-targeting anti-malarial antibodies. Kratochvil, S., Shen, C.H., Lin, Y.C. et al. Immunity (2021) 54:2859. DOI 10.1016/j.immuni.2021.10.017 · PubMed

Other PDB entries of the same protein (UniProt P02893 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WFY 1.23 Å, Crystal structure of Fab224 in complex with NPNA4 peptide from circumsporozoite protein
6WG0 1.6 Å, Crystal structure of Fab366 in complex with NPNA3 peptide from circumsporozoite protein
6AZM 1.6 Å, Crystal structure of the 580 germline antibody bound to circumsporozoite protein NANP…
6UC5 1.75 Å, Fab397 in complex with NPNA peptide
7RD4 1.75 Å, Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody…
6B5R 1.77 Å, Structure of PfCSP peptide 21 with human antibody CIS42
6B5M 1.79 Å, Structure of PfCSP peptide 21 with human protective antibody CIS43
6WFZ 1.84 Å, Crystal structure of Fab399 in complex with NPNA3 peptide from circumsporozoite protein
6D0X 1.85 Å, Crystal structure of chimeric H.2140 / K.1210 Fab in complex with circumsporozoite…
6UUD 1.85 Å, Crystal structure of antibody 5D5 in complex with PfCSP N-terminal peptide
6W00 1.85 Å, Crystal structure of Fab239 in complex with NPNA2 peptide from circumsporozoite protein
7RD9 1.91 Å, Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody…

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