9C79: Human monoclonal antibody MAD21-101

Human monoclonal antibody MAD21-101 bound to the N-terminus of cleaved circumsporozoite protein. Determined by X-ray diffraction at 1.46 Å resolution. Released 25 Dec 2024.

Method: X-ray diffraction
Resolution: 1.46 Å
Organisms: Homo sapiens, Plasmodium falciparum 3D7
Chains: 3
Atoms: 4,113
Mol. weight: 50.88 kDa
Released: 25 Dec 2024

Explore 9C79 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C79 contains 21 α-helices and 50 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 D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	97-99	3
α-helix	102	1
β-strand	103-104	2	4

Chain H: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	33-40	8	3
β-strand	44-52	9	3
β-strand	57-59	3	3
α-helix	64-66	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-98	11	3
β-strand	100C-100D	2	4
β-strand	100E-103	8	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	115-116	2
β-strand	117	1	5
α-helix	118-119	2
β-strand	120-124	5	6
α-helix	125-126	2
β-strand	127	1	7
β-strand	135-145	11	6
β-strand	146	1	5
β-strand	151-154	4	8
α-helix	155-157	3
β-strand	159	1	8
β-strand	163-165	3	6
α-helix	166-168	3
β-strand	169-170	2	6
β-strand	176-185	10	6
α-helix	186-188	3
β-strand	195-200	6	8
α-helix	201-203	3
β-strand	205-210	6	8
α-helix	212-213	2
β-strand	214	1	7

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-14	5	3
β-strand	19-25	7	9
β-strand	27C-27D	2	10
β-strand	30-31	2	10
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	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	84-90	7	3
α-helix	96	1
β-strand	97-98	2	3
β-strand	102-107	6	3
β-strand	111	1	11
α-helix	112-113	2
β-strand	114-118	5	12
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	12
β-strand	140	1	11
β-strand	145-150	6	13
β-strand	153-154	2	13
α-helix	155	1
β-strand	159-163	5	12
α-helix	164-167	4
β-strand	173-182	10	12
α-helix	183-187	5
β-strand	191-198	8	13
β-strand	201-208	8	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Monoclonal antibody MAD21-101 Fab Heavy Chain	H	protein	228	Homo sapiens
Monoclonal antibody MAD21-101 Fab Light Chain	L	protein	218	Homo sapiens
Circumsporozoite protein	D	protein	18	Plasmodium falciparum 3D7	Q7K740 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9C79_1 Monoclonal antibody MAD21-101 Fab Heavy Chain (chains H)
KVQLQESGPGQVKPSETLSLTCSVSGASVTVDYWSWIRQTPERGLEWIGYISYTGRTNYN
PSLKSRVTISTDTAKNQVSLKLSSVTAADTAVYYCTRDRSECPDGSCFAYVMAVWGHGTT
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (L), FASTA

>9C79_2 Monoclonal antibody MAD21-101 Fab Light Chain (chains L)
DIVMTQSPESLAVSLGERATINCKSNQSLLYSSTNKNYLVWYLQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYLSPLTFGGGTTVEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

Sequence of entity 3 (D), FASTA

>9C79_3 Circumsporozoite protein (chains D)
QPADGNPDPNANPNVDPN

Primary citation

Protective antibodies target cryptic epitope unmasked by cleavage of malaria sporozoite protein. Dacon, C., Moskovitz, R., Swearingen, K. et al. Science (2025) 387:eadr0510-eadr0510. DOI 10.1126/science.adr0510 · 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
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
7LKB 1.8 Å, Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody…

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