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- EMDB-7898: recombinant, shortened Plasmodium falciparum Circumsporozoite Pro... -

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Basic information

Entry
Database: EMDB / ID: EMD-7898
Titlerecombinant, shortened Plasmodium falciparum Circumsporozoite Protein (CSP) in complex with immunoglobulin g (IgG) 311 .
Map dataRecombinant, shortened circumsporozoite protein in complex with immunoglobulin G 311 (IgG311)
Sample
  • Complex: Recombinant, shortened Plasmodium Falciparum Circumsprozoite Protein (CSP) in complex with Immunoglobulin G (IgG) 311
    • Organelle or cellular component: Recombinant, shortened Plasmodium Falciparum Circumsprozoite Protein (CSP)
    • Organelle or cellular component: Immunoglobulin G (IgG) 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 13, 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: 0.0179
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0179
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7898.png

Downloads & links

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Map

FileDownload / File: emd_7898.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRecombinant, shortened circumsporozoite protein in complex with immunoglobulin G 311 (IgG311)
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: 0.0179 / Movie #1: 0.0179
Minimum - Maximum-0.044625543 - 0.08244537
Average (Standard dev.)0.00018091414 (±0.003991191)
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-0.0450.0820.000

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Supplemental data

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Sample components

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Entire : Recombinant, shortened Plasmodium Falciparum Circumsprozoite Prot...

EntireName: Recombinant, shortened Plasmodium Falciparum Circumsprozoite Protein (CSP) in complex with Immunoglobulin G (IgG) 311
Components
  • Complex: Recombinant, shortened Plasmodium Falciparum Circumsprozoite Protein (CSP) in complex with Immunoglobulin G (IgG) 311
    • Organelle or cellular component: Recombinant, shortened Plasmodium Falciparum Circumsprozoite Protein (CSP)
    • Organelle or cellular component: Immunoglobulin G (IgG) 311

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Supramolecule #1: Recombinant, shortened Plasmodium Falciparum Circumsprozoite Prot...

SupramoleculeName: Recombinant, shortened Plasmodium Falciparum Circumsprozoite Protein (CSP) in complex with Immunoglobulin G (IgG) 311
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Recombinant, shortened Plasmodium Falciparum Circumsprozoite Prot...

SupramoleculeName: Recombinant, shortened Plasmodium Falciparum Circumsprozoite 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: Immunoglobulin G (IgG) 311

SupramoleculeName: Immunoglobulin G (IgG) 311 / type: organelle_or_cellular_component / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

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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: 199 / 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: 18583
Final reconstructionNumber classes used: 1 / 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: 4732
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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