[English] 日本語
Yorodumi
- EMDB-8952: PTEX Core Complex in the Resetting (Compact) State -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8952
TitlePTEX Core Complex in the Resetting (Compact) State
Map dataPTEX Core Complex in the Resetting (Compact) State
Sample
  • Complex: Plasmodium Translocon of Exported Proteins (PTEX) Core Complex
    • Protein or peptide: Unknown (Claw)
    • Protein or peptide: Heat shock protein 101
    • Protein or peptide: Exported protein 2
    • Protein or peptide: Endogenous cargo polypeptide
    • Protein or peptide: Translocon component PTEX150
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsTranslocon / Membrane Protein / ATPase / PROTEIN TRANSPORT
Function / homology
Function and homology information


PTEX complex / apical complex / symbiont-containing vacuole / translocation of peptides or proteins into host cell cytoplasm / 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
Heat shock protein 101 / Exported protein 2 / Translocon component PTEX150
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote) / Plasmodium falciparum (isolate 3D7) (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.23 Å
AuthorsHo C / Lai M
Funding support United States, 11 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI094386 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 Heart, Lung, and Blood Institute (NIH/NHLBI)K99/R00 HL133453 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007323 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)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, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseAug 22, 2018-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0405
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0405
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6e11
  • Surface level: 0.0405
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8952.png

Downloads & links

-
Map

FileDownload / File: emd_8952.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPTEX Core Complex in the Resetting (Compact) State
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0405 / Movie #1: 0.0405
Minimum - Maximum-0.0696483 - 0.13130198
Average (Standard dev.)0.00032971794 (±0.0034134754)
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-0.0700.1310.000

-
Supplemental data

-
Additional map: PTEX Core Complex in the Resetting (Compact) State, additional map #1

Fileemd_8952_additional.map
AnnotationPTEX Core Complex in the Resetting (Compact) State, additional map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Plasmodium Translocon of Exported Proteins (PTEX) Core Complex

EntireName: Plasmodium Translocon of Exported Proteins (PTEX) Core Complex
Components
  • Complex: Plasmodium Translocon of Exported Proteins (PTEX) Core Complex
    • Protein or peptide: Unknown (Claw)
    • Protein or peptide: Heat shock protein 101
    • Protein or peptide: Exported protein 2
    • Protein or peptide: Endogenous cargo polypeptide
    • Protein or peptide: Translocon component PTEX150
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

-
Supramolecule #1: Plasmodium Translocon of Exported Proteins (PTEX) Core Complex

SupramoleculeName: Plasmodium Translocon of Exported Proteins (PTEX) Core Complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)

-
Macromolecule #1: Unknown (Claw)

MacromoleculeName: Unknown (Claw) / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 5.124308 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

-
Macromolecule #2: Heat shock protein 101

MacromoleculeName: Heat shock protein 101 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
Molecular weightTheoretical: 103.031914 KDa
SequenceString: MTRRYLKYYI FVTLLFFVQV INNVLCAPDN KQEQGKYLNR TINILNAGKN IAKSYGHNKL KPIHILSALA KSDYGSTLFK ENNVNAANL KEYIDIALEQ TRAGAPLDNK SKIVNSAEVK ETLALAEAAA NKYKSPKVDV EHLLSGLSND ELVNEIFNEV Y LTDEAIKA ...String:
MTRRYLKYYI FVTLLFFVQV INNVLCAPDN KQEQGKYLNR TINILNAGKN IAKSYGHNKL KPIHILSALA KSDYGSTLFK ENNVNAANL KEYIDIALEQ TRAGAPLDNK SKIVNSAEVK ETLALAEAAA NKYKSPKVDV EHLLSGLSND ELVNEIFNEV Y LTDEAIKA ILKRKFEKTK KDKDGKTGTL YIEQFGSNMN EKVRNGKLQG IYGRDEEIRA IIESLLRYNK NSPVLVGNPG TG KTTIVEG LVYRIEKGDV PKELQGYTVI SLNFRKFTSG TSYRGEFETR MKNIIKELKN KKNKIILFVD EIHLLLGAGK AEG GTDAAN LLKPVLSKGE IKLIGATTIA EYRKFIESCS AFERRFEKIL VEPPSVDMTV KILRSLKSKY ENFYGINITD KALV AAAKI SDRFIKDRYL PDKAIDLLNK ACSFLQVQLS GKPRIIDVTE RDIERLSYEI STLEKDVDKV SKKKYNKLIK EFEEK KEQL KKYYEEYVIT GERLKRKKEI EKKLNDLKEL TQNYVYSNKE PPIELQNSLK EAQQKYLELY KETVAYVEAK THNAMN VDA VYQEHVSYIY LRDSGMPLGS LSFESSKGAL KLYNSLSKSI IGNEDIIKSL SDAVVKAATG MKDPEKPIGT FLFLGPT GV GKTELAKTLA IELFNSKDNL IRVNMSEFTE AHSVSKITGS PPGYVGFSDS GQLTEAVREK PHSVVLFDEL EKAHADVF K VLLQILGDGY INDNHRRNID FSNTIIIMTS NLGAELFKKK LFFDADNSGT PEYKRVMEDV RLSLIKKCKK VFKPEFVNR IDKIGVFEPL NKKNLHKIVA LRFKKLEKRL EEKNIQVSVS EKAIDYIIDQ SYDPELGARP TLIFIESVIM TKFAIMYLKK ELVDDMDVF VDYNSKAKNL VINLSKT

UniProtKB: Heat shock protein 101

-
Macromolecule #3: Exported protein 2

MacromoleculeName: Exported protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
Molecular weightTheoretical: 33.458707 KDa
SequenceString: MKVSYIFSFF LLFFVYKNTN TVVCDNGYGD LAATSALTTV IKDPISLTIK DIYEHGVKNP FTKIIHKLKK FIRYRKVLRW SRMWWVLLV REIVGDNTIE KKTEKALREI WDQCTIAVYN NTLNAVESKP LLFLHGILNE CRNNFATKLR QDPSLIVAKI D QIIKSQIY ...String:
MKVSYIFSFF LLFFVYKNTN TVVCDNGYGD LAATSALTTV IKDPISLTIK DIYEHGVKNP FTKIIHKLKK FIRYRKVLRW SRMWWVLLV REIVGDNTIE KKTEKALREI WDQCTIAVYN NTLNAVESKP LLFLHGILNE CRNNFATKLR QDPSLIVAKI D QIIKSQIY RFWVSEPYLK IGRSHTLYTH ITPDAVPQLP KECTLKHLSS YMEEKLKSME SKKNIESGKY EFDVDSSETD ST KDDGKPD DDDDDDDNFD DDDNFDDDTV EEEDASGDLF KNEKKDENKE

UniProtKB: Exported protein 2

-
Macromolecule #4: Endogenous cargo polypeptide

MacromoleculeName: Endogenous cargo polypeptide / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 528.644 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

-
Macromolecule #5: Translocon component PTEX150

MacromoleculeName: Translocon component PTEX150 / type: protein_or_peptide / ID: 5 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
Molecular weightTheoretical: 112.523328 KDa
SequenceString: MRIIILALLI VCTIINYYCA VQNNGNKSLN VMPTCSMPGN DSDSNDNETG DVDNDKNNEL GNANDNNEMN NENAESKNMQ GENSNNQEQ LNENVHANDD AMYEGTPSSD NPPQENVDAN NNEQEYGPPQ EEPVSENNVE NVEVATDDSG NDNINNNDNF N NNDNYNDN ...String:
MRIIILALLI VCTIINYYCA VQNNGNKSLN VMPTCSMPGN DSDSNDNETG DVDNDKNNEL GNANDNNEMN NENAESKNMQ GENSNNQEQ LNENVHANDD AMYEGTPSSD NPPQENVDAN NNEQEYGPPQ EEPVSENNVE NVEVATDDSG NDNINNNDNF N NNDNYNDN DNFNEEPPSD DGNKNEDELT EGNQSDDKPM NEEEATINEM GKITNPFEDM LKGKVDDMDI GKMMNKDNLQ SF LSSLTGN KDGSGKNPLS DMMNIFGVPQ TGKEGAEGGV NKENQMKQIN ELKDKLETML KGAGVNVDKI KDSIKNNDLL KNK QLLKEA ISKLTLDPSM MNMLNNKDGA NGKPFDINPD SMMKMFNALS NENGNLDDLK MKPTDGSFDS FNDGVDNNLV PSNP KGQNN NEEDDEEGGD DDDYDDKSFV VNSKYADNSF EDKFNTFDEK DDDVKYELFG ENEEAEELNN NTTTASSKGD ANNSV NTQE GEGEEESFSA NEENINNNNN HNNKNYNNYN TSQQEEDDNS FNENDEPLIS SSQFDNNKKN KMSVSTHNKK SKNLMD SLD LESTNYGSNS SSSMSNNYNS KNKNSKKNNK KKSSQKDYIR TDGKVSFDMA TLQKTIKNFG GADNEIVQNI LKKYVTI DN DDDNDADEDE DEDDDDDDDL DEDEFSVKDI KKLIEEGILD YEDLTENELR KLAKPDDNFY ELSPYASDEK DLSLNETS G LTNEQLKNFL GQNGTYHMSY DSKSIDYAKQ KKSEKKEDQQ EDDDGFYDAY KQIKNSYDGI PNNFNHEAPQ LIGNNYVFT SIYDTKENLI KFLKKNSEYD LYDDDDKEGG NFKSPLYDKY GGKLQKFKRQ RAFNILKQWR AKEKKLKEKK KKEEMEENKE FDFSKNYNF SSKNDGGVTM FSKDQLEDMV KNFGGKPSAH VTDSFSRKEN PFVPTNTKNN SNDDDDMDNG YVTFDGKNKV S ENDDDEKG NNNDDENDND DSNDEEELDE EEDDN

UniProtKB: Translocon component PTEX150

-
Macromolecule #6: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 12 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridSupport film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsPTEX core complex purified from P. falciparum parasites cultured in human erythrocytes

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: -10 eV / Energy filter - Upper energy threshold: 10 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 2-50 / Average exposure time: 10.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1508462
Startup modelType of model: NONE
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 78499
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION (ver. 2.0)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6e11:
PTEX Core Complex in the Resetting (Compact) State

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more