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- PDB-6x87: CryoEM structure of the Plasmodium berghei circumsporozoite prote... -

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Basic information

Entry
Database: PDB / ID: 6x87
TitleCryoEM structure of the Plasmodium berghei circumsporozoite protein in complex with inhibitory mouse antibody 3D11.
Components
  • 3D11 Fab heavy chain
  • 3D11 Fab kappa chain
  • Circumsporozoite protein
KeywordsIMMUNE SYSTEM / antibody / malaria
Function / homology
Function and homology information


positive regulation of developmental process / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Circumsporozoite protein / Circumsporozoite protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Plasmodium berghei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKucharska, I. / Thai, E. / Rubinstein, J. / Julien, J.P.
Funding support Canada, 4items
OrganizationGrant numberCountry
Other governmentCIFAR Azrieli Global Scholar program Canada
Other governmentOntario Early Researcher Award program Canada
Other governmentCanada Research Chair program Canada
Other governmentCanadian Institutes of Health Research Canada
CitationJournal: Elife / Year: 2020
Title: Structural ordering of the circumsporozoite protein repeats by inhibitory antibody 3D11.
Authors: Iga Kucharska / Elaine Thai / Ananya Srivastava / John L Rubinstein / Régis Pomès / Jean-Philippe Julien /
Abstract: Plasmodium sporozoites express circumsporozoite protein (CSP) on their surface, an essential protein that contains central repeating motifs. Antibodies targeting this region can neutralize infection, ...Plasmodium sporozoites express circumsporozoite protein (CSP) on their surface, an essential protein that contains central repeating motifs. Antibodies targeting this region can neutralize infection, and the partial efficacy of RTS,S/AS01 - the leading malaria vaccine against (Pf) - has been associated with the humoral response against the repeats. Although structural details of antibody recognition of PfCSP have recently emerged, the molecular basis of antibody-mediated inhibition of other Plasmodium species via CSP binding remains unclear. Here, we analyze the structure and molecular interactions of potent monoclonal antibody (mAb) 3D11 binding to CSP (PbCSP) using molecular dynamics simulations, X-ray crystallography, and cryoEM. We reveal that mAb 3D11 can accommodate all subtle variances of the PbCSP repeating motifs, and, upon binding, induces structural ordering of PbCSP through homotypic interactions. Together, our findings uncover common mechanisms of antibody evolution in mammals against the CSP repeats of Plasmodium sporozoites.
History
DepositionJun 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
K: 3D11 Fab heavy chain
L: 3D11 Fab kappa chain
X: Circumsporozoite protein
M: 3D11 Fab heavy chain
N: 3D11 Fab kappa chain
I: 3D11 Fab heavy chain
J: 3D11 Fab kappa chain
G: 3D11 Fab heavy chain
H: 3D11 Fab kappa chain
E: 3D11 Fab heavy chain
F: 3D11 Fab kappa chain
C: 3D11 Fab heavy chain
D: 3D11 Fab kappa chain
A: 3D11 Fab heavy chain
B: 3D11 Fab kappa chain


Theoretical massNumber of molelcules
Total (without water)365,54715
Polymers365,54715
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area40210 Å2
ΔGint-225 kcal/mol
Surface area129170 Å2

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Components

#1: Antibody
3D11 Fab heavy chain


Mass: 22830.475 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
3D11 Fab kappa chain


Mass: 24191.020 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein Circumsporozoite protein


Mass: 36397.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (eukaryote) / Gene: CS / Production host: Homo sapiens (human) / References: UniProt: D1L8V5, UniProt: P06915*PLUS
Has protein modificationY

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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 berghei CSP protein and 3D11 FabCOMPLEXall0RECOMBINANT
23D11 Fab heavy chain, 3D11 Fab kappa chainCOMPLEX#1-#21RECOMBINANT
3Circumsporozoite proteinCOMPLEX#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23Plasmodiidae sp. (eukaryote)2605378
12Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTRIS(HOCH2)2CNH21
2150 mMsodium chlorideNaCl1
30.02 %sodium azideNaN31
40.01 %n-dodecyl beta-D-maltosideC24H46O111
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE / Humidity: 90 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 42.7 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2080

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18rc5_3822refinement
PHENIX1.18rc5_3822refinement
EM software
IDNameVersionCategory
2EPU2image acquisition
4cryoSPARC2CTF correction
7UCSF Chimera1.14model fitting
9PHENIX1.18model refinement
12cryoSPARC2classification
13cryoSPARC23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 669223
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 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: 10.96 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00223723
ELECTRON MICROSCOPYf_angle_d0.516832302
ELECTRON MICROSCOPYf_chiral_restr0.04033687
ELECTRON MICROSCOPYf_plane_restr0.00534111
ELECTRON MICROSCOPYf_dihedral_angle_d15.92648456

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