6B5S: PfCSP peptide 25 with human antibody CIS42

Structure of PfCSP peptide 25 with human antibody CIS42. Determined by X-ray diffraction at 1.98 Å resolution. Released 21 Mar 2018.

Method: X-ray diffraction
Resolution: 1.98 Å
Organisms: Homo sapiens, Plasmodium Falciparum
Chains: 3
Atoms: 3,661
Mol. weight: 49.25 kDa
Ligands: IPA
Released: 21 Mar 2018

Explore 6B5S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6B5S contains 16 α-helices and 45 β-strands across 2 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 H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
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	45-51	7	2
β-strand	57-59	3	2
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	100A-103	5	2
β-strand	107-111	5	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	186-188	3
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	6
β-strand	9-13	4	7
β-strand	19-25	7	6
α-helix	27A-27C	3
β-strand	33-38	6	7
β-strand	45-48	4	7
β-strand	49	1	8
β-strand	53	1	8
α-helix	54-55	2
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-91	8	7
β-strand	96-98	3	7
β-strand	102-106	5	7
β-strand	112	1	9
α-helix	113-114	2
β-strand	115-119	5	10
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	10
β-strand	141	1	9
β-strand	146-151	6	11
β-strand	154-156	3	11
β-strand	160-162	3	10
α-helix	163-165	3
β-strand	166-167	2	10
β-strand	173-181	9	10
α-helix	183-188	6
β-strand	192-198	7	11
β-strand	201-207	7	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CIS42 Fab Heavy chain	H	protein	222	Homo sapiens
CIS42 Fab Light chain	L	protein	216	Homo sapiens
pfCSP peptide 25: ASN-VAL-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-ASN	A	protein	15	Plasmodium Falciparum	P02893 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6B5S_1 CIS42 Fab Heavy chain (chains H)
QVQLVQSGSELKKPGASVKVSCKTSGYTFTTYAMNWVRQAPGQGLEWMGWINTNTGNPTY
APGFTGRFVFSFDTSVSTAYLQISSLKAEDTAVYYCARVYSYGVPFDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (L), FASTA

>6B5S_2 CIS42 Fab Light chain (chains L)
QSVLTQPASVSGSPGQSITISCTATSSNVGSFNLVSWYQHHPGKAPKLIIHEVSKRPSGA
SNRFSGSKSGNTASLTISGLQAEDEADYYCCSYVGSDTWVFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (A), FASTA

>6B5S_3 pfCSP peptide 25: ASN-VAL-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP-PRO-ASN (chains A)
NVDPNANPNVDPNAN

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	9

Water and common crystallization additives (NA, NH4) are not listed.

Primary citation

A human monoclonal antibody prevents malaria infection by targeting a new site of vulnerability on the parasite. Kisalu, N.K., Idris, A.H., Weidle, C. et al. Nat Med (2018) 24:408-416. DOI 10.1038/nm.4512 · 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
7RD3 1.81 Å, Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody…
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

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