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Yorodumi- EMDB-9065: Cryo-EM structure of the circumsporozoite protein of Plasmodium f... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9065 | |||||||||
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Title | Cryo-EM structure of the circumsporozoite protein of Plasmodium falciparum with a vaccine-elicited antibody reveals maturation of inter-antibody contacts | |||||||||
Map data | 311 Fab in complex with Plasmodium falciparum recombinant shortened CSP construct (rsCSP) | |||||||||
Sample |
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Function / homology | Function and homology information host cell surface binding / symbiont entry into host / entry into host cell by a symbiont-containing vacuole / heparan sulfate proteoglycan binding / immunoglobulin complex / side of membrane / adaptive immune response / cell surface / extracellular region / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.37 Å | |||||||||
Authors | Torres JL / Cottrell CA / Ward AB | |||||||||
Citation | Journal: Sci Adv / Year: 2018 Title: Cryo-EM structure of circumsporozoite protein with a vaccine-elicited antibody is stabilized by somatically mutated inter-Fab contacts. Authors: David Oyen / Jonathan L Torres / Christopher A Cottrell / C Richter King / Ian A Wilson / Andrew B Ward / Abstract: The circumsporozoite protein (CSP) on the surface of sporozoites is important for parasite development, motility, and host hepatocyte invasion. However, intrinsic disorder of the NANP repeat ...The circumsporozoite protein (CSP) on the surface of sporozoites is important for parasite development, motility, and host hepatocyte invasion. However, intrinsic disorder of the NANP repeat sequence in the central region of CSP has hindered its structural and functional characterization. Here, the cryo-electron microscopy structure at ~3.4-Å resolution of a recombinant shortened CSP construct with the variable domains (Fabs) of a highly protective monoclonal antibody reveals an extended spiral conformation of the central NANP repeat region surrounded by antibodies. This unusual structure appears to be stabilized and/or induced by interaction with an antibody where contacts between adjacent Fabs are somatically mutated and enhance the interaction. This maturation in non-antigen contact residues may be an effective mechanism for antibodies to target tandem repeat sequences and provide novel insights into malaria vaccine design. | |||||||||
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_9065.map.gz | 85.3 MB | EMDB map data format | |
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Header (meta data) | emd-9065-v30.xml emd-9065.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9065_fsc.xml | 10.3 KB | Display | FSC data file |
Images | emd_9065.png | 91.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9065 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9065 | HTTPS FTP |
-Validation report
Summary document | emd_9065_validation.pdf.gz | 511.8 KB | Display | EMDB validaton report |
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Full document | emd_9065_full_validation.pdf.gz | 511.4 KB | Display | |
Data in XML | emd_9065_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | emd_9065_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9065 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9065 | HTTPS FTP |
-Related structure data
Related structure data | 6mb3MC 7897C 7898C 7899C 9114C 6mhgC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9065.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 311 Fab in complex with Plasmodium falciparum recombinant shortened CSP construct (rsCSP) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 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 : Fab311 in complex with Plasmodium falciparum recombinant shortened CSP
Entire | Name: Fab311 in complex with Plasmodium falciparum recombinant shortened CSP |
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Components |
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-Supramolecule #1: Fab311 in complex with Plasmodium falciparum recombinant shortened CSP
Supramolecule | Name: Fab311 in complex with Plasmodium falciparum recombinant shortened CSP type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: shortened CSP
Supramolecule | Name: shortened CSP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Plasmodium falciparum (malaria parasite P. falciparum) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: Fab311
Supramolecule | Name: Fab311 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Plasmodium falciparum recombinant shortened CSP
Macromolecule | Name: Plasmodium falciparum recombinant shortened CSP / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Plasmodium falciparum (malaria parasite P. falciparum) |
Molecular weight | Theoretical: 30.232156 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: YGSSSNTRVL NELNYDNAGT NLYNELEMNY YGKQENWYSL KKNSRSLGEN DDGNNEDNEK LRKPKHKKLK QPADGNPDPN ANPNVDPNA NPNVDPNANP NVDPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP N ANPNANPN ...String: YGSSSNTRVL NELNYDNAGT NLYNELEMNY YGKQENWYSL KKNSRSLGEN DDGNNEDNEK LRKPKHKKLK QPADGNPDPN ANPNVDPNA NPNVDPNANP NVDPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP N ANPNANPN KNNQGNGQGH NMPNDPNRNV DENANANSAV KNNNNEEPSD KHIKEYLNKI QNSLSTEWSP CSVTCGNGIQ VR IKPGSAN KPKDELDYAN DIEKKICKME KCSSVFNVVN S |
-Macromolecule #2: Fab311 heavy chain
Macromolecule | Name: Fab311 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.098877 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG VVPPGRSLRL SCATSGFTFS NYGMHWVRQA PGKGLEWVAI IWYDGSRNFY AASVEGRFTI SRDNSKNTLY LQMNSLRVE DTAVYYCARA AYYDTSGYGD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String: EVQLVESGGG VVPPGRSLRL SCATSGFTFS NYGMHWVRQA PGKGLEWVAI IWYDGSRNFY AASVEGRFTI SRDNSKNTLY LQMNSLRVE DTAVYYCARA AYYDTSGYGD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCD |
-Macromolecule #3: Fab311 light chain
Macromolecule | Name: Fab311 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.980484 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ESVLTQPPSV SGAPGQTVTI SCTGGSSNIG AGYDVHWYQQ LPGTAPKLLI YGNINRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSYDRRLSG SWVFGGGTKL TVLGQPKAAP SVTLFPPSSE ELQANKATLV CLVSDFYPGA VTVAWKADGS P VKVGVETT ...String: ESVLTQPPSV SGAPGQTVTI SCTGGSSNIG AGYDVHWYQQ LPGTAPKLLI YGNINRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSYDRRLSG SWVFGGGTKL TVLGQPKAAP SVTLFPPSSE ELQANKATLV CLVSDFYPGA VTVAWKADGS P VKVGVETT KPSKQSNNKY AASSYLSLTP EQWKSHRSYS CRVTHEGSTV EKTVAPAECS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: C-flat-2/2 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 0-47 / Number grids imaged: 1 / Number real images: 1497 / Average exposure time: 12.0 sec. / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: OTHER / Target criteria: EMRinger | ||||||||
Output model | PDB-6mb3: |