6AZM

Crystal structure of the 580 germline antibody bound to circumsporozoite protein NANP 5-mer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Natural Parasite Exposure Induces Protective Human Anti-Malarial Antibodies.

Triller, G.Scally, S.W.Costa, G.Pissarev, M.Kreschel, C.Bosch, A.Marois, E.Sack, B.K.Murugan, R.Salman, A.M.Janse, C.J.Khan, S.M.Kappe, S.H.I.Adegnika, A.A.Mordmuller, B.Levashina, E.A.Julien, J.P.Wardemann, H.

(2017) Immunity 47: 1197-1209.e10

  • DOI: 10.1016/j.immuni.2017.11.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Antibodies against the NANP repeat of circumsporozoite protein (CSP), the major surface antigen of Plasmodium falciparum (Pf) sporozoites, can protect from malaria in animal models but protective humoral immunity is difficult to induce in humans. Her ...

    Antibodies against the NANP repeat of circumsporozoite protein (CSP), the major surface antigen of Plasmodium falciparum (Pf) sporozoites, can protect from malaria in animal models but protective humoral immunity is difficult to induce in humans. Here we cloned and characterized rare affinity-matured human NANP-reactive memory B cell antibodies elicited by natural Pf exposure that potently inhibited parasite transmission and development in vivo. We unveiled the molecular details of antibody binding to two distinct protective epitopes within the NANP repeat. NANP repeat recognition was largely mediated by germline encoded and immunoglobulin (Ig) heavy-chain complementarity determining region 3 (HCDR3) residues, whereas affinity maturation contributed predominantly to stabilizing the antigen-binding site conformation. Combined, our findings illustrate the power of exploring human anti-CSP antibody responses to develop tools for malaria control in the mammalian and the mosquito vector and provide a molecular basis for the structure-based design of next-generation CSP malaria vaccines.


    Organizational Affiliation

    Centre de Recherches Médicales de Lambaréné, Lambaréné, 242, Gabon; Institute of Tropical Medicine and German Center for Infection Research, partner site Tübingen, University of Tübingen, Tübingen, 72074, Germany; Leiden University Medical Centre (LUMC), Leiden, 2333 ZA, The Netherlands.,Institute of Tropical Medicine and German Center for Infection Research, partner site Tübingen, University of Tübingen, Tübingen, 72074, Germany.,Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands.,Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, 10117, Germany.,UPR9022 CNRS, U963 Inserm, Université de Strasbourg, Strasbourg, 67000, France.,B Cell Immunology, German Cancer Research Center, Heidelberg, 69120, Germany. Electronic address: h.wardemann@dkfz-heidelberg.de.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada; Departments of Biochemistry and Immunology, University of Toronto, ON M5G 0A4, Canada. Electronic address: jean-philippe.julien@sickkids.ca.,B Cell Immunology, German Cancer Research Center, Heidelberg, 69120, Germany.,Seattle Biomedical Research Institute, Seattle, WA 98109, USA.,The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK; Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
580 germline antibody, light chain
A, C
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
580 germline antibody, heavy chain
B, D
225N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Circumsporozoite protein NANP 5-mer
F, E
20Plasmodium falciparumMutation(s): 0 
Find proteins for P02893 (Plasmodium falciparum)
Go to UniProtKB:  P02893
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.961α = 90.00
b = 166.555β = 90.00
c = 72.996γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SHELXPREPdata scaling
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references