6D01

Crystal structure of 1210 Fab in complex with circumsporozoite protein NANP5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Antihomotypic affinity maturation improves human B cell responses against a repetitive epitope.

Imkeller, K.Scally, S.W.Bosch, A.Marti, G.P.Costa, G.Triller, G.Murugan, R.Renna, V.Jumaa, H.Kremsner, P.G.Sim, B.K.L.Hoffman, S.L.Mordmuller, B.Levashina, E.A.Julien, J.P.Wardemann, H.

(2018) Science 360: 1358-1362

  • DOI: 10.1126/science.aar5304
  • Primary Citation of Related Structures:  
    6D01, 6D0X, 6D11

  • PubMed Abstract: 
  • Affinity maturation selects B cells expressing somatically mutated antibody variants with improved antigen-binding properties to protect from invading pathogens. We determined the molecular mechanism underlying the clonal selection and affinity maturation of human B cells expressing protective antibodies against the circumsporozoite protein of the malaria parasite Plasmodium falciparum (PfCSP) ...

    Affinity maturation selects B cells expressing somatically mutated antibody variants with improved antigen-binding properties to protect from invading pathogens. We determined the molecular mechanism underlying the clonal selection and affinity maturation of human B cells expressing protective antibodies against the circumsporozoite protein of the malaria parasite Plasmodium falciparum (PfCSP). We show in molecular detail that the repetitive nature of PfCSP facilitates direct homotypic interactions between two PfCSP repeat-bound monoclonal antibodies, thereby improving antigen affinity and B cell activation. These data provide a mechanistic explanation for the strong selection of somatic mutations that mediate homotypic antibody interactions after repeated parasite exposure in humans. Our findings demonstrate a different mode of antigen-mediated affinity maturation to improve antibody responses to PfCSP and presumably other repetitive antigens.


    Organizational Affiliation

    B Cell Immunology, German Cancer Research Institute, Heidelberg, Germany. h.wardemann@dkfz.de jean-philippe.julien@sickkids.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
1210 Antibody, heavy chainA, C, E, G226Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
1210 Antibody, Light chainB, D, F, H213Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NANP5I, J20Plasmodium falciparumMutation(s): 0 
UniProt
Find proteins for P02893 (Plasmodium falciparum)
Explore P02893 
Go to UniProtKB:  P02893
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth B], BA [auth B], BB [auth F], CB [auth F], FA [auth C], O [auth A], OA [auth D], TA [auth E]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth F] , CA [auth C] , DA [auth C] , DB [auth G] , EA [auth C] , EB [auth H] , FB [auth H] , GA [auth D] , 
AB [auth F], CA [auth C], DA [auth C], DB [auth G], EA [auth C], EB [auth H], FB [auth H], GA [auth D], GB [auth H], HA [auth D], HB [auth H], IA [auth D], IB [auth I], JA [auth D], JB [auth I], K [auth A], KA [auth D], KB [auth I], L [auth A], LA [auth D], LB [auth J], M [auth A], MA [auth D], N [auth A], NA [auth D], P [auth B], PA [auth E], Q [auth B], QA [auth E], R [auth B], RA [auth E], S [auth B], SA [auth E], T [auth B], U [auth B], UA [auth F], V [auth B], VA [auth F], W [auth B], WA [auth F], X [auth B], XA [auth F], Y [auth B], YA [auth F], Z [auth B], ZA [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.963α = 90
b = 150.856β = 94.81
c = 134.651γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-04
    Changes: Data collection, Database references