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- EMDB-8951: PTEX Core Complex in the Engaged (Extended) State -

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Basic information

Entry
Database: EMDB / ID: EMD-8951
TitlePTEX Core Complex in the Engaged (Extended) State
Map data
SamplePlasmodium Translocon of Exported Proteins (PTEX) Core Complex
  • Heat shock protein 101Heat shock response
  • Exported protein 2
  • Translocon component PTEX150
  • Endogenous cargo polypeptide
  • Unknown (Claw)
  • ligand
Function / homology
Function and homology information


PTEX complex / apical complex / symbiont-containing vacuole membrane / symbiont-containing vacuole / translocation of peptides or proteins into host cell cytoplasm / response to unfolded protein / cellular response to heat / response to heat / ATPase / ATP binding / cytoplasm
Similarity search - Function
Chaperonins clpA/B signature 2. / ClpA/B, conserved site 2 / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / Clp repeat (R) domain profile. / Clp amino terminal domain, pathogenicity island component / AAA lid domain / ClpA/ClpB, AAA lid domain / Clp, repeat (R) domain / Clp, N-terminal domain superfamily ...Chaperonins clpA/B signature 2. / ClpA/B, conserved site 2 / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / Clp repeat (R) domain profile. / Clp amino terminal domain, pathogenicity island component / AAA lid domain / ClpA/ClpB, AAA lid domain / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Heat shock protein 101 / Exported protein 2 / Translocon component PTEX150
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote) / isolate 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsHo C / Lai M / Zhou ZH
Funding support United States, 11 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI125983 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007323 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM071940 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01 DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI094386 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)K99/R00 HL133453 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
CitationJournal: Nature / Year: 2018
Title: Malaria parasite translocon structure and mechanism of effector export.
Authors: Chi-Min Ho / Josh R Beck / Mason Lai / Yanxiang Cui / Daniel E Goldberg / Pascal F Egea / Z Hong Zhou /
Abstract: The putative Plasmodium translocon of exported proteins (PTEX) is essential for transport of malarial effector proteins across a parasite-encasing vacuolar membrane into host erythrocytes, but the ...The putative Plasmodium translocon of exported proteins (PTEX) is essential for transport of malarial effector proteins across a parasite-encasing vacuolar membrane into host erythrocytes, but the mechanism of this process remains unknown. Here we show that PTEX is a bona fide translocon by determining structures of the PTEX core complex at near-atomic resolution using cryo-electron microscopy. We isolated the endogenous PTEX core complex containing EXP2, PTEX150 and HSP101 from Plasmodium falciparum in the 'engaged' and 'resetting' states of endogenous cargo translocation using epitope tags inserted using the CRISPR-Cas9 system. In the structures, EXP2 and PTEX150 interdigitate to form a static, funnel-shaped pseudo-seven-fold-symmetric protein-conducting channel spanning the vacuolar membrane. The spiral-shaped AAA+ HSP101 hexamer is tethered above this funnel, and undergoes pronounced compaction that allows three of six tyrosine-bearing pore loops lining the HSP101 channel to dissociate from the cargo, resetting the translocon for the next threading cycle. Our work reveals the mechanism of P. falciparum effector export, and will inform structure-based design of drugs targeting this unique translocon.
History
DepositionJul 8, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseAug 22, 2018-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6e10
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8951.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 480 pix.
= 499.2 Å
1.04 Å/pix.
x 480 pix.
= 499.2 Å
1.04 Å/pix.
x 480 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.0424 / Movie #1: 0.038
Minimum - Maximum-0.062355958 - 0.13751948
Average (Standard dev.)0.00031809916 (±0.0034089806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 499.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z499.200499.200499.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-69-50-137
NX/NY/NZ136114193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0620.1380.000

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Supplemental data

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Additional map: PTEX Core Complex in the Engaged (Extended) State, additional map #1

Fileemd_8951_additional_1.map
AnnotationPTEX Core Complex in the Engaged (Extended) State, additional map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: PTEX Core Complex in the Engaged (Extended) State, additional map #2

Fileemd_8951_additional_2.map
AnnotationPTEX Core Complex in the Engaged (Extended) State, additional map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Plasmodium Translocon of Exported Proteins (PTEX) Core Complex

EntireName: Plasmodium Translocon of Exported Proteins (PTEX) Core Complex
Number of components: 7

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Component #1: protein, Plasmodium Translocon of Exported Proteins (PTEX) Core C...

ProteinName: Plasmodium Translocon of Exported Proteins (PTEX) Core Complex
Recombinant expression: No
SourceSpecies: Plasmodium falciparum 3D7 (eukaryote)

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Component #2: protein, Heat shock protein 101

ProteinName: Heat shock protein 101Heat shock response / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 106.277125 kDa
SourceSpecies: isolate 3D7 (eukaryote)

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Component #3: protein, Exported protein 2

ProteinName: Exported protein 2 / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 33.458707 kDa
SourceSpecies: isolate 3D7 (eukaryote)

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Component #4: protein, Translocon component PTEX150

ProteinName: Translocon component PTEX150 / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 22.59317 kDa
SourceSpecies: isolate 3D7 (eukaryote)

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Component #5: protein, Endogenous cargo polypeptide

ProteinName: Endogenous cargo polypeptide / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.294587 kDa
SourceSpecies: isolate 3D7 (eukaryote)

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Component #6: protein, Unknown (Claw)

ProteinName: Unknown (Claw) / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 4.954098 kDa
SourceSpecies: isolate 3D7 (eukaryote)

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Component #7: ligand, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.523247 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 4000.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 72866
3D reconstructionSoftware: RELION / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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