6AXK

Crystal structure of Fab311 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.103 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 2.1 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: 10.1073/pnas.1715812114
  • Primary Citation of Related Structures:  

  • 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 con ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab311 heavy chain
A
224N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab311 light chain
B
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ACE-ASN-PRO-ASN-ALA-ASN-PRO-ASN-ALA-ASN-PRO-ASN
E
14Plasmodium falciparumMutation(s): 0 
Find proteins for P02893 (Plasmodium falciparum)
Go to UniProtKB:  P02893
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A, B
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A, B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
E
NON-POLYMERH2 N

--

PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLU
ACE
Query on ACE
E
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.103 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.117α = 90.00
b = 44.729β = 90.00
c = 186.079γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-09-07 
  • Released Date: 2017-11-22 
  • Deposition Author(s): Oyen, D., Wilson, I.A.

Revision History 

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 2.0: 2017-12-06
    Type: Atomic model, Database references
  • Version 2.1: 2017-12-13
    Type: Database references