[English] 日本語
Yorodumi
- EMDB-26936: Complex of Plasmodium falciparum circumsporozoite protein with 850 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26936
TitleComplex of Plasmodium falciparum circumsporozoite protein with 850 Fab
Map datamap of Plasmodium falciparum CSP in complex with 850 Fab.
Sample
  • Complex: complex of Plasmodium falciparum circumsporozoite protein with 850 Fab.
    • Complex: Plasmodium falciparum circumsporozoite protein
      • Protein or peptide: Circumsporozoite protein
    • Complex: 850 Fab
      • Protein or peptide: 850 Fab Heavy Chain
      • Protein or peptide: 850 Fab Light Chain
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 / side of membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function
Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKucharska I / Prieto K / Rubinstein JL / Julien JP
Funding support Canada, United States, 6 items
OrganizationGrant numberCountry
Ontario Early Researcher Awards Canada
Canada Foundation for Innovation Canada
Ontario Research Fund Canada
Canada Research Chairs Canada
Bill & Melinda Gates FoundationINV-008866 United States
CIFAR Azrieli Global Scholars Canada
CitationJournal: PLoS Pathog / Year: 2022
Title: High-density binding to Plasmodium falciparum circumsporozoite protein repeats by inhibitory antibody elicited in mouse with human immunoglobulin repertoire.
Authors: Iga Kucharska / Špela Binter / Rajagopal Murugan / Stephen W Scally / Julia Ludwig / Katherine Prieto / Elaine Thai / Giulia Costa / Kan Li / Gillian Q Horn / Yevel Flores-Garcia / ...Authors: Iga Kucharska / Špela Binter / Rajagopal Murugan / Stephen W Scally / Julia Ludwig / Katherine Prieto / Elaine Thai / Giulia Costa / Kan Li / Gillian Q Horn / Yevel Flores-Garcia / Alexandre Bosch / Taylor Sicard / John L Rubinstein / Fidel Zavala / S Moses Dennison / Georgia D Tomaras / Elena A Levashina / Paul Kellam / Hedda Wardemann / Jean-Philippe Julien /
Abstract: Antibodies targeting the human malaria parasite Plasmodium falciparum circumsporozoite protein (PfCSP) can prevent infection and disease. PfCSP contains multiple central repeating NANP motifs; some ...Antibodies targeting the human malaria parasite Plasmodium falciparum circumsporozoite protein (PfCSP) can prevent infection and disease. PfCSP contains multiple central repeating NANP motifs; some of the most potent anti-infective antibodies against malaria bind to these repeats. Multiple antibodies can bind the repeating epitopes concurrently by engaging into homotypic Fab-Fab interactions, which results in the ordering of the otherwise largely disordered central repeat into a spiral. Here, we characterize IGHV3-33/IGKV1-5-encoded monoclonal antibody (mAb) 850 elicited by immunization of transgenic mice with human immunoglobulin loci. mAb 850 binds repeating NANP motifs with picomolar affinity, potently inhibits Plasmodium falciparum (Pf) in vitro and, when passively administered in a mouse challenge model, reduces liver burden to a similar extent as some of the most potent anti-PfCSP mAbs yet described. Like other IGHV3-33/IGKV1-5-encoded anti-NANP antibodies, mAb 850 primarily utilizes its HCDR3 and germline-encoded aromatic residues to recognize its core NANP motif. Biophysical and cryo-electron microscopy analyses reveal that up to 19 copies of Fab 850 can bind the PfCSP repeat simultaneously, and extensive homotypic interactions are observed between densely-packed PfCSP-bound Fabs to indirectly improve affinity to the antigen. Together, our study expands on the molecular understanding of repeat-induced homotypic interactions in the B cell response against PfCSP for potently protective mAbs against Pf infection.
History
DepositionMay 9, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26936.png

Downloads & links

-
Map

FileDownload / File: emd_26936.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of Plasmodium falciparum CSP in complex with 850 Fab.
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.4575855 - 2.4939785
Average (Standard dev.)-0.003570106 (±0.07121606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 350.19998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map of Plasmodium falciparum CSP in complex with 850 Fab.

Fileemd_26936_half_map_1.map
Annotationhalf map of Plasmodium falciparum CSP in complex with 850 Fab.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map of Plasmodium falciparum CSP in complex with 850 Fab.

Fileemd_26936_half_map_2.map
Annotationhalf map of Plasmodium falciparum CSP in complex with 850 Fab.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : complex of Plasmodium falciparum circumsporozoite protein with 85...

EntireName: complex of Plasmodium falciparum circumsporozoite protein with 850 Fab.
Components
  • Complex: complex of Plasmodium falciparum circumsporozoite protein with 850 Fab.
    • Complex: Plasmodium falciparum circumsporozoite protein
      • Protein or peptide: Circumsporozoite protein
    • Complex: 850 Fab
      • Protein or peptide: 850 Fab Heavy Chain
      • Protein or peptide: 850 Fab Light Chain

-
Supramolecule #1: complex of Plasmodium falciparum circumsporozoite protein with 85...

SupramoleculeName: complex of Plasmodium falciparum circumsporozoite protein with 850 Fab.
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: Plasmodium falciparum circumsporozoite protein

SupramoleculeName: Plasmodium falciparum circumsporozoite protein / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

-
Supramolecule #3: 850 Fab

SupramoleculeName: 850 Fab / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: 850 Fab Heavy Chain

MacromoleculeName: 850 Fab Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.234037 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG VVQPGRSLRL SCAASGFTFS NFGMHWIRQS PGKGLEWVAI IWYDGSNTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCAKV WFGESEDNYS VDVWGQGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QVQLVESGGG VVQPGRSLRL SCAASGFTFS NFGMHWIRQS PGKGLEWVAI IWYDGSNTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCAKV WFGESEDNYS VDVWGQGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSC

-
Macromolecule #2: 850 Fab Light Chain

MacromoleculeName: 850 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.476045 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPST LSTSVGDRVT ITCRASQSIS NWLAWYQQKP GKAPKLLIYK ASTLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYSSYWTFGQ GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
DIQMTQSPST LSTSVGDRVT ITCRASQSIS NWLAWYQQKP GKAPKLLIYK ASTLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYSSYWTFGQ GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

-
Macromolecule #3: Circumsporozoite protein

MacromoleculeName: Circumsporozoite protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 39.986016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FQEYQCYGSS SNTRVLNELN YDNAGTNLYN ELEMNYYGKQ ENWYSLKKNS RSLGENDDGN NEDNEKLRKP KHKKLKQPAD GNPDPNANP NVDPNANPNV DPNANPNVDP NANPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP NANPNANPNA N PNANPNAN ...String:
FQEYQCYGSS SNTRVLNELN YDNAGTNLYN ELEMNYYGKQ ENWYSLKKNS RSLGENDDGN NEDNEKLRKP KHKKLKQPAD GNPDPNANP NVDPNANPNV DPNANPNVDP NANPNANPNA NPNANPNANP NANPNANPNA NPNANPNANP NANPNANPNA N PNANPNAN PNANPNANPN ANPNANPNAN PNANPNANPN ANPNANPNAN PNANPNANPN ANPNANPNAN PNANPNANPN AN PNANPNA NPNANPNKNN QGNGQGHNMP NDPNRNVDEN ANANSAVKNN NNEEPSDKHI KEYLNKIQNS LSTEWSPCSV TCG NGIQVR IKPGSANKPK DELDYANDIE KKICKMEKCS SVFNVVQSSP HHHHHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3TRIS
150.0 mMNaClSodium chlorideSodium chloride
GridModel: Homemade / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 4306 / Average electron dose: 45.24 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1295064
Initial angle assignmentType: OTHER
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 165747

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more