+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7068 | |||||||||
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Title | rsCSP + Fab311 Complex | |||||||||
Map data | rsCSP + Fab311 Complex | |||||||||
Sample |
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Biological species | Plasmodium falciparum (malaria parasite P. falciparum) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
Authors | Torres JL / Ward AB | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: Structural basis for antibody recognition of the NANP repeats in circumsporozoite protein. Authors: David Oyen / Jonathan L Torres / Ulrike Wille-Reece / Christian F Ockenhouse / Daniel Emerling / Jacob Glanville / Wayne Volkmuth / Yevel Flores-Garcia / Fidel Zavala / Andrew B Ward / C ...Authors: David Oyen / Jonathan L Torres / Ulrike Wille-Reece / Christian F Ockenhouse / Daniel Emerling / Jacob Glanville / Wayne Volkmuth / Yevel Flores-Garcia / Fidel Zavala / Andrew B Ward / C Richter King / Ian A Wilson / 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)- ...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 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) 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 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7068.map.gz | 11.8 MB | EMDB map data format | |
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Header (meta data) | emd-7068-v30.xml emd-7068.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
Images | emd_7068.png | 28 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7068 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7068 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7068.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | rsCSP + Fab311 Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex containing recombinant, shortened circumsporozite protein...
Entire | Name: Complex containing recombinant, shortened circumsporozite protein (CSP) and fragment antigen binding (Fab) 311 |
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Components |
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-Supramolecule #1: Complex containing recombinant, shortened circumsporozite protein...
Supramolecule | Name: Complex containing recombinant, shortened circumsporozite protein (CSP) and fragment antigen binding (Fab) 311 type: complex / ID: 1 / Parent: 0 Details: Plasmodium falciparum's circumsporozite protein in complex with Fab311, a protecting antibody from the RTS,S clinical trial |
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-Supramolecule #2: Complex containing recombinant, shortened circumsporozite protein...
Supramolecule | Name: Complex containing recombinant, shortened circumsporozite protein (CSP) type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 492 KDa |
-Supramolecule #3: Fragment antigen binding (Fab) 311
Supramolecule | Name: Fragment antigen binding (Fab) 311 / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Staining | Type: NEGATIVE / Material: 2% (w/v) Uranyl Formate Details: add 3 uL sample, blot, add 3 uL 2% uranyl formate, blot immediately, add 3 uL 2% uranyl formate, blot after 30 seconds | |||||||||
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CELLULOSE ACETATE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Details: 15 mA |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus min: 1.5 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 1 / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 6320 |
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Initial angle assignment | Type: PROJECTION MATCHING Projection matching processing - Number reference projections: 20 Software - Name: EMAN (ver. 2) / Software - details: e2initialmodel.py / Details: Used EMAN2 e2initialmodel |
Final 3D classification | Number classes: 3 / Avg.num./class: 7000 / Software - Name: RELION (ver. 2.0) |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 6320 |