6D01 | pdb_00006d01

Crystal structure of 1210 Fab in complex with circumsporozoite protein NANP5

• PDB DOI: https://doi.org/10.2210/pdb6D01/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Plasmodium falciparum
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2018-04-09 Released: 2018-06-13 
• Deposition Author(s): Scally, S.W., Bosch, A., Imkeller, K., Wardemann, H., Julien, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.227 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

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

• PubMed: 29880723 
• DOI: https://doi.org/10.1126/science.aar5304
• Primary Citation 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). 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.

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Organizational Affiliation: 
• B Cell Immunology, German Cancer Research Institute, Heidelberg, Germany.
Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada.
Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany.
Institute of Immunology, University Medical Center Ulm, Ulm, Germany.
Institute of Tropical Medicine and German Center for Infection Research, Partner Site Tübingen, University of Tübingen, Tübingen, Germany.
Sanaria, Rockville, MD, USA.
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada. [e-mail] [e-mail].
Departments of Biochemistry and Immunology, University of Toronto, Toronto, ON, Canada.
B Cell Immunology, German Cancer Research Institute, Heidelberg, Germany. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 198.95 kDa 
• Atom Count: 13,609 
• Modeled Residue Count: 1,768 
• Deposited Residue Count: 1,796 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1210 Antibody, heavy chain	A, C, E, G	226	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1210 Antibody, Light chain	B, D, F, H	213	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NANP5	I, J	20	Plasmodium falciparum	Mutation(s): 0
UniProt
Find proteins for P02893 (Plasmodium falciparum) Explore P02893  Go to UniProtKB:  P02893

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	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
EDO	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.227 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 205.963	α = 90
b = 150.856	β = 94.81
c = 134.651	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Scally, S.W., Bosch, A., Imkeller, K., Wardemann, H., Julien, J.P.

Revision History  

• 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
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary