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- EMDB-7897: Full-length Plasmodium falciparum Circumsporozoite Protein (CSP) ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7897
TitleFull-length Plasmodium falciparum Circumsporozoite Protein (CSP) in complex with fragment antigen binding (Fab) 311.
Map dataFull-length Plasmodium falciparum Circumsporozoite Protein (CSP) in complex with fragment antigen binding (Fab) 311.
Sample
  • Complex: Full-length Plasmodium falciparum Circumsporozoite Protein (CSP) in complex with fragment antigen binding (Fab) 311.
    • Organelle or cellular component: Full-length Plasmodium falciparum Circumsporozoite Protein (CSP)
    • Organelle or cellular component: Fragment antigen binding (Fab) 311
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 27.0 Å
AuthorsTorres JL / Ward AB
CitationJournal: 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
DepositionMay 23, 2018-
Header (metadata) releaseJun 6, 2018-
Map releaseApr 3, 2019-
UpdateApr 3, 2019-
Current statusApr 3, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0242
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0242
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7897.png

Downloads & links

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Map

FileDownload / File: emd_7897.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull-length Plasmodium falciparum Circumsporozoite Protein (CSP) in complex with fragment antigen binding (Fab) 311.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 224 pix.
= 459.2 Å		2.05 Å/pix.
x 224 pix.
= 459.2 Å		2.05 Å/pix.
x 224 pix.
= 459.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0242 / Movie #1: 0.0242
Minimum - Maximum-0.05385263 - 0.09037935
Average (Standard dev.)0.000074080366 (±0.004659974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 459.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z459.200459.200459.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0540.0900.000

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Supplemental data

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Sample components

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Entire : Full-length Plasmodium falciparum Circumsporozoite Protein (CSP) ...

EntireName: Full-length Plasmodium falciparum Circumsporozoite Protein (CSP) in complex with fragment antigen binding (Fab) 311.
Components
  • Complex: Full-length Plasmodium falciparum Circumsporozoite Protein (CSP) in complex with fragment antigen binding (Fab) 311.
    • Organelle or cellular component: Full-length Plasmodium falciparum Circumsporozoite Protein (CSP)
    • Organelle or cellular component: Fragment antigen binding (Fab) 311

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Supramolecule #1: Full-length Plasmodium falciparum Circumsporozoite Protein (CSP) ...

SupramoleculeName: Full-length Plasmodium falciparum Circumsporozoite Protein (CSP) in complex with fragment antigen binding (Fab) 311.
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Full-length Plasmodium falciparum Circumsporozoite Protein (CSP)

SupramoleculeName: Full-length Plasmodium falciparum Circumsporozoite Protein (CSP)
type: organelle_or_cellular_component / ID: 2 / Parent: 1
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Fragment antigen binding (Fab) 311

SupramoleculeName: Fragment antigen binding (Fab) 311 / type: organelle_or_cellular_component / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.4 / Details: 1X TBS pH 7.4
StainingType: NEGATIVE / Material: 2% Uranyl Formate
Details: add 3 uL sample, blot, add 3 uL 2% uranyl formate, blot immediately, add 3 uL 2% uranyl formate, blot after 30 seconds
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
DetailsGris screening performed on FEI Mogagni
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 1 / Number real images: 166 / Average exposure time: 0.5 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 25245
Final reconstructionNumber classes used: 50 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 4170
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2.1)

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