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- PDB-6e10: PTEX Core Complex in the Engaged (Extended) State -

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Basic information

Entry
Database: PDB / ID: 60000000000
TitlePTEX Core Complex in the Engaged (Extended) State
Components
  • Endogenous cargo polypeptide
  • Exported protein 2
  • Heat shock protein 101
  • Translocon component PTEX150
  • Unknown (Claw)
KeywordsPROTEIN TRANSPORT / Translocon / Membrane Protein / ATPase
Function / homology
Function and homology information


translocation of peptides or proteins into host cell cytoplasm / PTEX complex / apical complex / symbiont-containing vacuole / symbiont-containing vacuole membrane / response to unfolded protein / cellular response to heat / response to heat / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. ...ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Heat shock protein 101 / Exported protein 2 / Translocon component PTEX150
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Plasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsHo, C. / Lai, M. / Zhou, Z.H.
Funding support United States, 11items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI094386 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01 DE025567 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)K99/R00 HL133453 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 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 Allergy and Infectious Diseases (NIH/NIAID)R21 AI125983 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, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
1: Heat shock protein 101
2: Heat shock protein 101
3: Heat shock protein 101
4: Heat shock protein 101
5: Heat shock protein 101
6: Heat shock protein 101
B: Exported protein 2
a: Translocon component PTEX150
A: Exported protein 2
g: Translocon component PTEX150
G: Exported protein 2
f: Translocon component PTEX150
F: Exported protein 2
e: Translocon component PTEX150
E: Exported protein 2
d: Translocon component PTEX150
D: Exported protein 2
c: Translocon component PTEX150
C: Exported protein 2
b: Translocon component PTEX150
0: Endogenous cargo polypeptide
h: Translocon component PTEX150
i: Unknown (Claw)
j: Unknown (Claw)
k: Unknown (Claw)
l: Unknown (Claw)
m: Unknown (Claw)
n: Unknown (Claw)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,089,91740
Polymers1,083,63828
Non-polymers6,27912
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area155290 Å2
ΔGint-599 kcal/mol
Surface area308580 Å2

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Components

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Protein , 4 types, 27 molecules 123456BAGFEDCagfedcbhijklmn

#1: Protein
Heat shock protein 101


Mass: 106277.125 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum), (natural) Plasmodium falciparum 3D7 (eukaryote)
References: UniProt: Q8IIJ8
#2: Protein
Exported protein 2


Mass: 33458.707 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q8IKC8
#3: Protein
Translocon component PTEX150


Mass: 22593.170 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum), (natural) Plasmodium falciparum 3D7 (eukaryote)
References: UniProt: Q8ILA1
#5: Protein
Unknown (Claw)


Mass: 4954.098 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)

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Protein/peptide / Non-polymers , 2 types, 13 molecules 0

#4: Protein/peptide Endogenous cargo polypeptide


Mass: 1294.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote)
#6: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Plasmodium Translocon of Exported Proteins (PTEX) Core Complex
Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: PTEX core complex purified from P. falciparum parasites cultured in human erythrocytes
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 4000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 50 / Used frames/image: 2-50

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2Leginon3.2image acquisition
4CTFFINDCTFFIND4.1CTF correction
9cryoSPARCinitial Euler assignment
10RELIONfinal Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1508462
3D reconstructionResolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72866 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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