5BK3

Crystal structure of the neutralizing anti-circumsporozoite protein 580 antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 2.1 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: 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 Antibody, light chainA [auth L],
C [auth B],
E [auth D],
G [auth F]
220Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
580 Antibody, heavy chainB [auth H],
D [auth A],
F [auth C],
H [auth E]
228Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth G],
J [auth I]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth J]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth K]6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ
GlyCosmos:  G82348BZ
GlyGen:  G82348BZ
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth A]
EA [auth A]
IA [auth D]
JA [auth D]
NA [auth C]
DA [auth A],
EA [auth A],
IA [auth D],
JA [auth D],
NA [auth C],
P [auth L],
Q [auth L],
QA [auth F],
T [auth H],
X [auth B],
Y [auth B],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
FA [auth D]
GA [auth D]
AA [auth A],
BA [auth A],
CA [auth A],
FA [auth D],
GA [auth D],
HA [auth D],
KA [auth C],
LA [auth C],
M [auth L],
MA [auth C],
N [auth L],
O [auth L],
OA [auth F],
PA [auth F],
R [auth H],
RA [auth E],
S [auth H],
SA [auth E],
U [auth B],
V [auth B],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.364α = 90
b = 179.567β = 109.61
c = 140.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SHELXPREPdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary