6BQB | pdb_00006bqb

MGG4 Fab in complex with peptide

• PDB DOI: https://doi.org/10.2210/pdb6BQB/pdb

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


• Deposited: 2017-11-27 Released: 2018-03-07 
• Deposition Author(s): Oyen, D., Tan, J., Lanzavecchia, A., Wilson, I.A.
• Funding Organization(s): PATH's Malaria Vaccine Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.196 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

A public antibody lineage that potently inhibits malaria infection through dual binding to the circumsporozoite protein.

Tan, J., Sack, B.K., Oyen, D., Zenklusen, I., Piccoli, L., Barbieri, S., Foglierini, M., Fregni, C.S., Marcandalli, J., Jongo, S., Abdulla, S., Perez, L., Corradin, G., Varani, L., Sallusto, F., Sim, B.K.L., Hoffman, S.L., Kappe, S.H.I., Daubenberger, C., Wilson, I.A., Lanzavecchia, A.

(2018) Nat Med 24: 401-407

• PubMed: 29554084 
• DOI: https://doi.org/10.1038/nm.4513
• Primary Citation Related Structures: 
  6BQB


• PubMed Abstract: 
  

  Immunization with attenuated Plasmodium falciparum sporozoites (PfSPZs) has been shown to be protective against malaria, but the features of the antibody response induced by this treatment remain unclear. To investigate this response in detail, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized with repeated injection of Sanaria PfSPZ Vaccine and who were found to be protected from controlled human malaria infection with infectious homologous PfSPZs. All isolated IgG monoclonal antibodies bound to P. falciparum circumsporozoite protein (PfCSP) and recognized distinct epitopes in its N terminus, NANP-repeat region, and C terminus. Strikingly, the most effective antibodies, as determined in a humanized mouse model, bound not only to the repeat region, but also to a minimal peptide at the PfCSP N-terminal junction that is not in the RTS,S vaccine. These dual-specific antibodies were isolated from different donors and were encoded by VH3-30 or VH3-33 alleles that encode tryptophan or arginine at position 52. Using structural and mutational data, we describe the elements required for germline recognition and affinity maturation. Our study provides potent neutralizing antibodies and relevant information for lineage-targeted vaccine design and immunization strategies.

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Organizational Affiliation: 
• Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.
Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
Center for Infectious Disease Research, Seattle, Washington, USA.
Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California, USA.
Faculty of Science, University of Basel, Basel, Switzerland.
Swiss Tropical and Public Health Institute, Clinical Immunology Unit, Basel, Switzerland.
Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
Ifakara Health Institute, Bagamoyo Clinical Trial Unit, Bagamoyo, Tanzania.
Biochemistry Department, University of Lausanne, Epalinges, Switzerland.
Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
Sanaria Inc., Rockville, Maryland, USA.
Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, California, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content 

• Total Structure Weight: 49.94 kDa 
• Atom Count: 4,128 
• Modeled Residue Count: 448 
• Deposited Residue Count: 460 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MGG4 Fab light chain	A [auth L]	220	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MGG4 Fab heavy chain	B [auth H]	224	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal junction peptide	C [auth P]	16	Plasmodium falciparum	Mutation(s): 0
UniProt
Find proteins for Q7K740 (Plasmodium falciparum (isolate 3D7)) Explore Q7K740  Go to UniProtKB:  Q7K740

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth L], E [auth L], F [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	B [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.196 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.782	α = 90
b = 68.062	β = 90
c = 148.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Oyen, D., Tan, J., Lanzavecchia, A., Wilson, I.A.

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Funding Organization	Location	Grant Number
PATH's Malaria Vaccine Initiative	United States	--

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection, Database references
• Version 1.2: 2018-04-25
  Changes: Data collection, Database references
• Version 2.0: 2024-11-20
  Changes: Data collection, Database references, Polymer sequence, Structure summary