7SG5 | pdb_00007sg5

Structure of PfCSP peptide 21 with antibody CIS43_Var2

• PDB DOI: https://doi.org/10.2210/pdb7SG5/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-10-05 Released: 2022-06-22 
• Deposition Author(s): Tripathi, P., Kwong, P.D.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.218 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Highly protective antimalarial antibodies via precision library generation and yeast display screening.

Banach, B.B., Tripathi, P., Da Silva Pereira, L., Gorman, J., Nguyen, T.D., Dillon, M., Fahad, A.S., Kiyuka, P.K., Madan, B., Wolfe, J.R., Bonilla, B., Flynn, B., Francica, J.R., Hurlburt, N.K., Kisalu, N.K., Liu, T., Ou, L., Rawi, R., Schon, A., Shen, C.H., Teng, I.T., Zhang, B., Pancera, M., Idris, A.H., Seder, R.A., Kwong, P.D., DeKosky, B.J.

(2022) J Exp Medicine 219

• PubMed: 35736810 
• DOI: https://doi.org/10.1084/jem.20220323
• Primary Citation Related Structures: 
  7SG5, 7SG6


• PubMed Abstract: 
  

  The monoclonal antibody CIS43 targets the Plasmodium falciparum circumsporozoite protein (PfCSP) and prevents malaria infection in humans for up to 9 mo following a single intravenous administration. To enhance the potency and clinical utility of CIS43, we used iterative site-saturation mutagenesis and DNA shuffling to screen precise gene-variant yeast display libraries for improved PfCSP antigen recognition. We identified several mutations that improved recognition, predominately in framework regions, and combined these to produce a panel of antibody variants. The most improved antibody, CIS43_Var10, had three mutations and showed approximately sixfold enhanced protective potency in vivo compared to CIS43. Co-crystal and cryo-electron microscopy structures of CIS43_Var10 with the peptide epitope or with PfCSP, respectively, revealed functional roles for each of these mutations. The unbiased site-directed mutagenesis and screening pipeline described here represent a powerful approach to enhance protective potency and to enable broader clinical use of antimalarial antibodies.

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Organizational Affiliation: 
• Bioengineering Graduate Program, The University of Kansas, Lawrence, KS.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD.
Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS.
Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA.
Department of Biology, Johns Hopkins University, Baltimore, MD.
Department of Chemical Engineering, The University of Kansas, Lawrence, KS.
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA.
The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.59 kDa 
• Atom Count: 3,854 
• Modeled Residue Count: 451 
• Deposited Residue Count: 461 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CIS43_Var2 Fab Heavy chain	A [auth H]	226	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CIS43_Var2 Fab Light chain	B [auth L]	220	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PfCSP peptide 21	C [auth A]	15	synthetic construct	Mutation(s): 0
UniProt
Find proteins for Q7K740 (Plasmodium falciparum (isolate 3D7)) Explore Q7K740  Go to UniProtKB:  Q7K740

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth H], F [auth L], G [auth L], H [auth L], I [auth L]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.218 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.77	α = 90
b = 61.137	β = 106.56
c = 75.313	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Tripathi, P., Kwong, P.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2023-07-05
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary