+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20774 | |||||||||
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Title | Fab397 in complex with NPNA8 peptide (Class 3) | |||||||||
Map data | Fab397 in complex with NPNA8 peptide (Class 3) | |||||||||
Sample |
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Biological species | Homo sapiens (human) / Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 27.0 Å | |||||||||
Authors | Ward AB / Torres JL | |||||||||
Funding support | United States, 1 items
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Citation | Journal: J Mol Biol / Year: 2020 Title: Diverse Antibody Responses to Conserved Structural Motifs in Plasmodium falciparum Circumsporozoite Protein. Authors: Tossapol Pholcharee / David Oyen / Jonathan L Torres / Yevel Flores-Garcia / Gregory M Martin / Gonzalo E González-Páez / Daniel Emerling / Wayne Volkmuth / Emily Locke / C Richter King / ...Authors: Tossapol Pholcharee / David Oyen / Jonathan L Torres / Yevel Flores-Garcia / Gregory M Martin / Gonzalo E González-Páez / Daniel Emerling / Wayne Volkmuth / Emily Locke / C Richter King / Fidel Zavala / Andrew B Ward / Ian A Wilson / Abstract: Malaria vaccine candidate RTS,S/AS01 is based on the central and C-terminal regions of the circumsporozoite protein (CSP) of P. falciparum. mAb397 was isolated from a volunteer in an RTS,S/AS01 ...Malaria vaccine candidate RTS,S/AS01 is based on the central and C-terminal regions of the circumsporozoite protein (CSP) of P. falciparum. mAb397 was isolated from a volunteer in an RTS,S/AS01 clinical trial, and it protects mice from infection by malaria sporozoites. However, mAb397 originates from the less commonly used VH3-15 germline gene compared to the VH3-30/33 antibodies generally elicited by RTS,S to the central NANP repeat region of CSP. The crystal structure of mAb397 with an NPNA peptide shows that the central NPNA forms a type I β-turn and is the main recognition motif. In most anti-NANP antibodies studied to date, a germline-encoded Trp is used to engage the Pro in NPNA β-turns, but here the Trp interacts with the first Asn. This "conserved" Trp, however, can arise from different germline genes and be located in the heavy or the light chain. Variation in the terminal ψ angles of the NPNA β-turns results in different dispositions of the subsequent NPNA and, hence, different stoichiometries and modes of antibody binding to rsCSP. Diverse protective antibodies against NANP repeats are therefore not limited to a single germline gene response or mode of binding. | |||||||||
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_20774.map.gz | 14.8 MB | EMDB map data format | |
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Header (meta data) | emd-20774-v30.xml emd-20774.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20774_fsc.xml | 7.5 KB | Display | FSC data file |
Images | emd_20774.png | 51 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20774 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20774 | HTTPS FTP |
-Validation report
Summary document | emd_20774_validation.pdf.gz | 77.5 KB | Display | EMDB validaton report |
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Full document | emd_20774_full_validation.pdf.gz | 76.6 KB | Display | |
Data in XML | emd_20774_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20774 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20774 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20774.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Fab397 in complex with NPNA8 peptide (Class 3) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Fragment antigen binding (Fab) 397 in complex with NPNA8 peptide ...
Entire | Name: Fragment antigen binding (Fab) 397 in complex with NPNA8 peptide (Class 3) |
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Components |
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-Supramolecule #1: Fragment antigen binding (Fab) 397 in complex with NPNA8 peptide ...
Supramolecule | Name: Fragment antigen binding (Fab) 397 in complex with NPNA8 peptide (Class 3) type: complex / ID: 1 / Parent: 0 |
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Molecular weight | Theoretical: 150 KDa |
-Supramolecule #2: fragment antigen binding (fab) 397
Supramolecule | Name: fragment antigen binding (fab) 397 / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: NPNA8 Peptide
Supramolecule | Name: NPNA8 Peptide / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Plasmodium falciparum (malaria parasite P. falciparum) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-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% Uranyl Formate | |||||||||
Grid | Support film - Material: CELLULOSE ACETATE / Support film - topology: CONTINUOUS / Details: unspecified |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 1 / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |