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- EMDB-22089: CryoEM structure of the Plasmodium berghei circumsporozoite prote... -

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Basic information

Entry
Database: EMDB / ID: EMD-22089
TitleCryoEM structure of the Plasmodium berghei circumsporozoite protein in complex with inhibitory mouse antibody 3D11.
Map dataCircumsporozoite protein in complex with inhibitory antibody 3D11.
Sample
  • Complex: Complex of Plasmodium berghei CSP protein and 3D11 Fab
    • Complex: 3D11 Fab heavy chain, 3D11 Fab kappa chain
      • Protein or peptide: 3D11 Fab heavy chain
      • Protein or peptide: 3D11 Fab kappa chain
    • Complex: Circumsporozoite protein
      • Protein or peptide: Circumsporozoite protein
Keywordsantibody / malaria / IMMUNE SYSTEM
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
Similarity search - Domain/homology
Circumsporozoite protein / Circumsporozoite protein
Similarity search - Component
Biological speciesMus musculus (house mouse) / Plasmodiidae sp. (eukaryote) / Plasmodium berghei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKucharska I / Thai E
Funding support Canada, 4 items
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, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6x87
  • Surface level: 3.7
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6x87
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22089.png

Downloads & links

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Map

FileDownload / File: emd_22089.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCircumsporozoite protein in complex with inhibitory antibody 3D11.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.7 / Movie #1: 3.7
Minimum - Maximum-31.469335999999998 - 48.388415999999999
Average (Standard dev.)-0.000000000006099 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z339.200339.200339.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-31.46948.388-0.000

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Supplemental data

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Sample components

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Entire : Complex of Plasmodium berghei CSP protein and 3D11 Fab

EntireName: Complex of Plasmodium berghei CSP protein and 3D11 Fab
Components
  • Complex: Complex of Plasmodium berghei CSP protein and 3D11 Fab
    • Complex: 3D11 Fab heavy chain, 3D11 Fab kappa chain
      • Protein or peptide: 3D11 Fab heavy chain
      • Protein or peptide: 3D11 Fab kappa chain
    • Complex: Circumsporozoite protein
      • Protein or peptide: Circumsporozoite protein

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Supramolecule #1: Complex of Plasmodium berghei CSP protein and 3D11 Fab

SupramoleculeName: Complex of Plasmodium berghei CSP protein and 3D11 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: 3D11 Fab heavy chain, 3D11 Fab kappa chain

SupramoleculeName: 3D11 Fab heavy chain, 3D11 Fab kappa chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: Circumsporozoite protein

SupramoleculeName: Circumsporozoite protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Plasmodiidae sp. (eukaryote)

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Macromolecule #1: 3D11 Fab heavy chain

MacromoleculeName: 3D11 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.830475 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NSQAYLQQSG AELVRSGASV KMSCKASGYT FTSYNMHWVK QTPGQGLEWI GYIYPGNGVT NFNQKFKGKA TLTADTSSST AYMQISSLT SEDSAVYFCA SAAYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA L TSGVHTFP ...String:
NSQAYLQQSG AELVRSGASV KMSCKASGYT FTSYNMHWVK QTPGQGLEWI GYIYPGNGVT NFNQKFKGKA TLTADTSSST AYMQISSLT SEDSAVYFCA SAAYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA L TSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSC

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Macromolecule #2: 3D11 Fab kappa chain

MacromoleculeName: 3D11 Fab kappa chain / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.19102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NSDVVMTQTP LTLSVTIGQP ASISCKSSQS LLYSDGKTYL NWLLQRPGQS PKRLISLVSE LDSGVPDRFT GSGSGTDFTL KISRVEAED LGVYYCWQGT HFPRTFGGGT KLEIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN A LQSGNSQE ...String:
NSDVVMTQTP LTLSVTIGQP ASISCKSSQS LLYSDGKTYL NWLLQRPGQS PKRLISLVSE LDSGVPDRFT GSGSGTDFTL KISRVEAED LGVYYCWQGT HFPRTFGGGT KLEIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN A LQSGNSQE SVTEQDSKDS TYSLSSTLTL SKADYEKHKV YACEVTHQGL SSPVTKSFNR GEC

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Macromolecule #3: Circumsporozoite protein

MacromoleculeName: Circumsporozoite protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium berghei (eukaryote)
Molecular weightTheoretical: 36.397008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EFATMGILPS PGMPALLSLV SLLSVLLMGC VAQQKSIQAQ RNLNELCYNE GNDNKLYHVL NSKNGKIYNR NTVNRLLADA PEGKKNEKK NEKIERNNKL KQPPPPPNPN DPPPPNPNDP PPPNPNDPPP PNPNDPPPPN ANDPPPPNAN DPAPPNANDP A PPNANDPA ...String:
EFATMGILPS PGMPALLSLV SLLSVLLMGC VAQQKSIQAQ RNLNELCYNE GNDNKLYHVL NSKNGKIYNR NTVNRLLADA PEGKKNEKK NEKIERNNKL KQPPPPPNPN DPPPPNPNDP PPPNPNDPPP PNPNDPPPPN ANDPPPPNAN DPAPPNANDP A PPNANDPA PPNANDPAPP NANDPPPPNP NDPAPPNAND PPPPNPNDPA PPQGNNNPQP QPRPQPQPQP QPQPQPQPQP QP RPQPQPQ PGGNNNNKNN NNDDSYIPSA EKILEFVKQI RDSITEEWSQ CQVTCGSGIR VRKRKGSNKK AEDLTLEDID TEI CKMDKC SPHHHHHH

UniProtKB: Circumsporozoite protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mM(HOCH2)2CNH2TRIS
150.0 mMNaClsodium chloride
0.02 %NaN3sodium azide
0.01 %C24H46O11n-dodecyl beta-D-maltoside
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2080 / Average electron dose: 42.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 669223
Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 165747
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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