6X8S

Crystal structure of 3D11 Fab in complex with Plasmodium berghei circumsporozoite protein NAND peptide

  • Classification: IMMUNE SYSTEM
  • Organism(s): Mus musculus, Plasmodium berghei ANKA
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2020-06-01 Released: 2020-12-02 
  • Deposition Author(s): Thai, E., Julien, J.P.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), CIFAR Azrieli Global Scholar, Ontario Early Researcher Award, Canada Research Chair

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural ordering of the Plasmodium berghei circumsporozoite protein repeats by inhibitory antibody 3D11.

Kucharska, I.Thai, E.Srivastava, A.Rubinstein, J.L.Pomes, R.Julien, J.P.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.59018
  • Primary Citation of Related Structures:  
    6X87, 6X8P, 6X8Q, 6X8S, 6X8U

  • PubMed Abstract: 

    Plasmodium sporozoites express circumsporozoite protein (CSP) on their surface, an essential protein that contains central repeating motifs. Antibodies targeting this region can neutralize infection, and the partial efficacy of RTS,S/AS01 - the leading malaria vaccine against P. falciparum (Pf) - has been associated with the humoral response against the repeats. Although structural details of antibody recognition of PfCSP have recently emerged, the molecular basis of antibody-mediated inhibition of other Plasmodium species via CSP binding remains unclear. Here, we analyze the structure and molecular interactions of potent monoclonal antibody (mAb) 3D11 binding to P. berghei CSP (PbCSP) using molecular dynamics simulations, X-ray crystallography, and cryoEM. We reveal that mAb 3D11 can accommodate all subtle variances of the PbCSP repeating motifs, and, upon binding, induces structural ordering of PbCSP through homotypic interactions. Together, our findings uncover common mechanisms of antibody evolution in mammals against the CSP repeats of Plasmodium sporozoites.


  • Organizational Affiliation

    Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3D11 Fab heavy chainA [auth H]215Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
3D11 Fab light chainB [auth L]219Mus musculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NAND peptideC [auth P]16Plasmodium berghei ANKAMutation(s): 0 
UniProt
Find proteins for P23093 (Plasmodium berghei (strain Anka))
Explore P23093 
Go to UniProtKB:  P23093
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23093
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth L]
BA [auth L]
CA [auth L]
D [auth H]
DA [auth P]
AA [auth L],
BA [auth L],
CA [auth L],
D [auth H],
DA [auth P],
E [auth H],
F [auth H],
G [auth H],
H,
I [auth H],
J [auth H],
K [auth H],
L [auth H],
M [auth H],
N [auth H],
O [auth H],
P [auth L],
Q [auth L],
R [auth L],
S [auth L],
T [auth L],
U [auth L],
V [auth L],
W [auth L],
X [auth L],
Y [auth L],
Z [auth L]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.651α = 90
b = 59.651β = 90
c = 234.901γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesACB-12002
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAGM-12006
CIFAR Azrieli Global ScholarCanada--
Ontario Early Researcher AwardCanada--
Canada Research ChairCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Refinement description