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- EMDB-7899: Recombinant, shortened Plasmodium falciparum Cisrcumsporozoite Pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-7899
TitleRecombinant, shortened Plasmodium falciparum Cisrcumsporozoite Protein (rsCSP) in complex with fragment antigen binding (Fab) 317
Map dataRecombinant, shortened Plasmodium Falciparum Circumsporozoite Protein (rsCSP) in complex with fragment antigen binding (Fab) 317
Sample
  • Complex: Recombinant, shortened Plasmodium Falciparum Cisrcumsporozoite Protein (rsCSP) in complex with fragment antigen binding (Fab) 317
    • Organelle or cellular component: Recombinant, shortened Plasmodium Falciparum Cisrcumsporozoite Protein (rsCSP)
    • Organelle or cellular component: fragment antigen binding (Fab) 317
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsTorres JL / Oyen D
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: 0.168
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.168
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7899.png

Downloads & links

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Map

FileDownload / File: emd_7899.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRecombinant, shortened Plasmodium Falciparum Circumsporozoite Protein (rsCSP) in complex with fragment antigen binding (Fab) 317
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 288 pix.
= 331.2 Å		1.15 Å/pix.
x 288 pix.
= 331.2 Å		1.15 Å/pix.
x 288 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.168 / Movie #1: 0.168
Minimum - Maximum-0.34126827 - 0.9754897
Average (Standard dev.)-0.0022295443 (±0.047251184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 331.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z331.200331.200331.200
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/NS288288288
D min/max/mean-0.3410.975-0.002

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Supplemental data

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Sample components

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Entire : Recombinant, shortened Plasmodium Falciparum Cisrcumsporozoite Pr...

EntireName: Recombinant, shortened Plasmodium Falciparum Cisrcumsporozoite Protein (rsCSP) in complex with fragment antigen binding (Fab) 317
Components
  • Complex: Recombinant, shortened Plasmodium Falciparum Cisrcumsporozoite Protein (rsCSP) in complex with fragment antigen binding (Fab) 317
    • Organelle or cellular component: Recombinant, shortened Plasmodium Falciparum Cisrcumsporozoite Protein (rsCSP)
    • Organelle or cellular component: fragment antigen binding (Fab) 317

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Supramolecule #1: Recombinant, shortened Plasmodium Falciparum Cisrcumsporozoite Pr...

SupramoleculeName: Recombinant, shortened Plasmodium Falciparum Cisrcumsporozoite Protein (rsCSP) in complex with fragment antigen binding (Fab) 317
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Recombinant, shortened Plasmodium Falciparum Cisrcumsporozoite Pr...

SupramoleculeName: Recombinant, shortened Plasmodium Falciparum Cisrcumsporozoite Protein (rsCSP)
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) 317

SupramoleculeName: fragment antigen binding (Fab) 317 / 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.4
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force: 0 Wait time: 10s Blot time: 4.5s.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 0-47 / Number grids imaged: 1 / Number real images: 470 / Average electron dose: 5.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC / Number images used: 17714
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC

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