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- PDB-7v05: Complex of Plasmodium falciparum circumsporozoite protein with 850 Fab -

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Basic information

Entry
Database: PDB / ID: 7v05
TitleComplex of Plasmodium falciparum circumsporozoite protein with 850 Fab
Components
  • 850 Fab Heavy Chain
  • 850 Fab Light Chain
  • Circumsporozoite protein
KeywordsANTIMICROBIAL PROTEIN / IMMUNE SYSTEM/CELL INVASION / antibody / malaria / Plasmodium falciparum / circumsporozoite protein / IMMUNE SYSTEM-CELL INVASION complex
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 speciesMus musculus (house mouse)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKucharska, I. / Prieto, K. / Rubinstein, J.L. / Julien, J.P.
Funding support Canada, United States, 6items
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, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 850 Fab Heavy Chain
a: 850 Fab Light Chain
B: 850 Fab Heavy Chain
b: 850 Fab Light Chain
C: 850 Fab Heavy Chain
c: 850 Fab Light Chain
D: 850 Fab Heavy Chain
d: 850 Fab Light Chain
E: 850 Fab Heavy Chain
e: 850 Fab Light Chain
F: 850 Fab Heavy Chain
f: 850 Fab Light Chain
G: 850 Fab Heavy Chain
g: 850 Fab Light Chain
H: 850 Fab Heavy Chain
h: 850 Fab Light Chain
X: Circumsporozoite protein
I: 850 Fab Heavy Chain
i: 850 Fab Light Chain
J: 850 Fab Heavy Chain
j: 850 Fab Light Chain
K: 850 Fab Heavy Chain
k: 850 Fab Light Chain
L: 850 Fab Heavy Chain
l: 850 Fab Light Chain
M: 850 Fab Heavy Chain
m: 850 Fab Light Chain
N: 850 Fab Heavy Chain
n: 850 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)707,92729
Polymers707,92729
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody
850 Fab Heavy Chain


Mass: 24234.037 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
850 Fab Light Chain


Mass: 23476.045 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein Circumsporozoite protein / / CS / PfCSP


Mass: 39986.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CSP, PF3D7_0304600 / Production host: Homo sapiens (human) / References: UniProt: Q7K740
Sequence detailsThe Pro-Asn-Ala-Asn at positions 177-180 in the sequence is actually Pro-Asn-Val-Asp. However, not ...The Pro-Asn-Ala-Asn at positions 177-180 in the sequence is actually Pro-Asn-Val-Asp. However, not all of the protein is visible in the map, and it cannot be determined where the Pro-Asn-Val-Asp segments are in the model. Therefore, it was all modeled as Pro-Asn-Ala-Asn. The actual sequence of this protein is: FQEYQCYGSSSNTRVLNELNYDNAGTNLYNELEMNYYGKQENWYSLKKNSRSLGENDDGN NEDNEKLRKPKHKKLKQPADGNPDPNANPNVDPNANPNVDPNANPNVDPNANPNANPNAN PNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNVD PNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNAN PNANPNANPNANPNKNNQGNGQGHNMPNDPNRNVDENANANSAVKNNNNEEPSDKHIKEY LNKIQNSLSTEWSPCSVTCGNGIQVRIKPGSANKPKDELDYANDIEKKICKMEKCSSVFN VVQSSPHHHHHH

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1complex of Plasmodium falciparum circumsporozoite protein with 850 Fab.COMPLEXall0RECOMBINANT
2Plasmodium falciparum circumsporozoite proteinCOMPLEX#31RECOMBINANT
3850 FabCOMPLEX#1-#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Plasmodium falciparum (malaria parasite P. falciparum)5833
43Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTRISC4H11NO31
2150 mMSodium chlorideNaClSodium chloride1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45.24 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 4306

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
2EPU2image acquisition
4cryoSPARC2CTF correction
7UCSF Chimeramodel fitting
11cryoSPARC2classification
12cryoSPARC23D reconstruction
13PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1295064
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 165747 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 40.27 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007948529
ELECTRON MICROSCOPYf_angle_d0.607766093
ELECTRON MICROSCOPYf_chiral_restr0.0467405
ELECTRON MICROSCOPYf_plane_restr0.00478452
ELECTRON MICROSCOPYf_dihedral_angle_d10.498417188

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