6AXL | pdb_00006axl

Crystal structure of Fab317 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.217 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 6AXL

This is version 1.4 of the entry. See complete history

Literature

Structural basis for antibody recognition of the NANP repeats in Plasmodium falciparum circumsporozoite protein.

Oyen, D.Torres, J.L.Wille-Reece, U.Ockenhouse, C.F.Emerling, D.Glanville, J.Volkmuth, W.Flores-Garcia, Y.Zavala, F.Ward, A.B.King, C.R.Wilson, I.A.

(2017) Proc Natl Acad Sci U S A 114: E10438-E10445

  • DOI: https://doi.org/10.1073/pnas.1715812114
  • Primary Citation Related Structures: 
    6AXK, 6AXL

  • PubMed Abstract: 

    Acquired resistance against antimalarial drugs has further increased the need for an effective malaria vaccine. The current leading candidate, RTS,S, is a recombinant circumsporozoite protein (CSP)-based vaccine against Plasmodium falciparum that contains 19 NANP repeats followed by a thrombospondin repeat domain. Although RTS,S has undergone extensive clinical testing and has progressed through phase III clinical trials, continued efforts are underway to enhance its efficacy and duration of protection. Here, we determined that two monoclonal antibodies (mAbs 311 and 317), isolated from a recent controlled human malaria infection trial exploring a delayed fractional dose, inhibit parasite development in vivo by at least 97%. Crystal structures of antibody fragments (Fabs) 311 and 317 with an (NPNA) 3 peptide illustrate their different binding modes. Notwithstanding, one and three of the three NPNA repeats adopt similar well-defined type I β-turns with Fab311 and Fab317, respectively. Furthermore, to explore antibody binding in the context of P. falciparum CSP, we used negative-stain electron microscopy on a recombinant shortened CSP (rsCSP) construct saturated with Fabs. Both complexes display a compact rsCSP with multiple Fabs bound, with the rsCSP-Fab311 complex forming a highly organized helical structure. Together, these structural insights may aid in the design of a next-generation malaria vaccine.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.

Macromolecule Content 

  • Total Structure Weight: 97.14 kDa 
  • Atom Count: 7,188 
  • Modeled Residue Count: 886 
  • Deposited Residue Count: 900 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab317 light chainsA [auth C],
C [auth B]
214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab317 heavy chainB [auth D],
D [auth A]
222Homo sapiensMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptide ACE-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-NH2E [auth G],
F [auth I]
14Plasmodium 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.217 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.663α = 90
b = 65.342β = 106.4
c = 99.043γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2017-12-13
    Changes: Database references
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary