6AZM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.immuni.2017.11.007
  • Primary Citation of Related Structures:  
    5BK0, 5BK3, 5BK5, 6AZM, 6AZX

  • 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. 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

    B Cell Immunology, German Cancer Research Center, Heidelberg, 69120, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
580 germline antibody, light chain
A, C
219Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
580 germline antibody, heavy chain
B, D
225Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Circumsporozoite protein NANP 5-merE [auth F],
F [auth E]
20Plasmodium falciparumMutation(s): 0 
UniProt
Find proteins for P02893 (Plasmodium falciparum)
Explore P02893 
Go to UniProtKB:  P02893
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02893
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.961α = 90
b = 166.555β = 90
c = 72.996γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SHELXPREPdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Refinement description