[English] 日本語
Yorodumi
- PDB-9bax: PI4KA complex bound to C-terminus of EFR3A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bax
TitlePI4KA complex bound to C-terminus of EFR3A
Components
  • Hyccin
  • Phosphatidylinositol 4-kinase alpha
  • Protein EFR3 homolog A
  • Tetratricopeptide repeat protein 7B
KeywordsSIGNALING PROTEIN / PI4KA / TTC7B / FAM126A / EFR3A / EFR3 / Lipid Signaling / PI4KIIIa / Phosphoinositide Kinase
Function / homology
Function and homology information


reorganization of cellular membranes to establish viral sites of replication / Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Schwann cell migration / Synthesis of PIPs at the Golgi membrane / modulation by host of viral process / Golgi-associated vesicle membrane / myelination in peripheral nervous system / phosphatidylinositol biosynthetic process ...reorganization of cellular membranes to establish viral sites of replication / Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Schwann cell migration / Synthesis of PIPs at the Golgi membrane / modulation by host of viral process / Golgi-associated vesicle membrane / myelination in peripheral nervous system / phosphatidylinositol biosynthetic process / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / myelination / protein localization to plasma membrane / actin cytoskeleton organization / neuron projection / cadherin binding / focal adhesion / signal transduction / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / EFR3, armadillo repeat / PI4-kinase, N-terminal / PI4-kinase N-terminal region / Hyccin / Tetratricopeptide repeat protein 7, N-terminal / Hyccin / Tetratricopeptide repeat protein 7 N-terminal / : ...: / : / EFR3, armadillo repeat / PI4-kinase, N-terminal / PI4-kinase N-terminal region / Hyccin / Tetratricopeptide repeat protein 7, N-terminal / Hyccin / Tetratricopeptide repeat protein 7 N-terminal / : / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Tetratricopeptide repeat / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Phosphatidylinositol 4-kinase alpha / Protein EFR3 homolog A / Tetratricopeptide repeat protein 7B / Hyccin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsShaw, A.L. / Suresh, S. / Yip, C.K. / Burke, J.E.
Funding support Canada, 4items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)NSERC-2020-04241 Canada
Canadian Institutes of Health Research (CIHR)PJT-168907 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-03951 Canada
Canadian Institutes of Health Research (CIHR)PJT-195808 Canada
CitationJournal: Sci Adv / Year: 2024
Title: Molecular basis for plasma membrane recruitment of PI4KA by EFR3.
Authors: Sushant Suresh / Alexandria L Shaw / Joshua G Pemberton / Mackenzie K Scott / Noah J Harris / Matthew A H Parson / Meredith L Jenkins / Pooja Rohilla / Alejandro Alvarez-Prats / Tamas Balla ...Authors: Sushant Suresh / Alexandria L Shaw / Joshua G Pemberton / Mackenzie K Scott / Noah J Harris / Matthew A H Parson / Meredith L Jenkins / Pooja Rohilla / Alejandro Alvarez-Prats / Tamas Balla / Calvin K Yip / John E Burke /
Abstract: The lipid kinase phosphatidylinositol 4 kinase III α (PI4KIIIα/PI4KA) is a master regulator of the lipid composition and asymmetry of the plasma membrane. PI4KA exists primarily in a heterotrimeric ...The lipid kinase phosphatidylinositol 4 kinase III α (PI4KIIIα/PI4KA) is a master regulator of the lipid composition and asymmetry of the plasma membrane. PI4KA exists primarily in a heterotrimeric complex with its regulatory proteins TTC7 and FAM126. Fundamental to PI4KA activity is its targeted recruitment to the plasma membrane by the lipidated proteins EFR3A and EFR3B. Here, we report a cryogenic electron microscopy structure of the C terminus of EFR3A bound to the PI4KA-TTC7B-FAM126A complex, with extensive validation using both hydrogen deuterium exchange mass spectrometry, and mutational analysis. The EFR3A C terminus undergoes a disorder-order transition upon binding to the PI4KA complex, with an unexpected direct interaction with both TTC7B and FAM126A. Complex disrupting mutations in TTC7B, FAM126A, and EFR3 decrease PI4KA recruitment to the plasma membrane. Multiple posttranslational modifications and disease linked mutations map to this site, providing insight into how PI4KA membrane recruitment can be regulated and disrupted in human disease.
History
DepositionApr 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2May 21, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Protein EFR3 homolog A
B: Phosphatidylinositol 4-kinase alpha
F: Tetratricopeptide repeat protein 7B
G: Hyccin
H: Protein EFR3 homolog A
A: Phosphatidylinositol 4-kinase alpha
D: Tetratricopeptide repeat protein 7B
E: Hyccin


Theoretical massNumber of molelcules
Total (without water)760,8048
Polymers760,8048
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Protein EFR3 homolog A / Protein EFR3-like


Mass: 14366.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: EFR3A c-terminus construct (721-791) / Source: (gene. exp.) Homo sapiens (human) / Gene: EFR3A, KIAA0143 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q14156
#2: Protein Phosphatidylinositol 4-kinase alpha / PI4-kinase alpha / PI4K-alpha / PtdIns-4-kinase alpha / Phosphatidylinositol 4-Kinase III alpha


Mass: 237102.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KA, PIK4, PIK4CA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P42356, 1-phosphatidylinositol 4-kinase
#3: Protein Tetratricopeptide repeat protein 7B / TPR repeat protein 7B / Tetratricopeptide repeat protein 7-like-1 / TPR repeat protein 7-like-1


Mass: 94294.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTC7B, TTC7L1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86TV6
#4: Protein Hyccin / Down-regulated by CTNNB1 protein A


Mass: 34638.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Truncated construct (1-308) / Source: (gene. exp.) Homo sapiens (human) / Gene: HYCC1, DRCTNNB1A, FAM126A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BYI3
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Dimer of heterotetramers of PI4KA,TTC7B,FAM126A, and EFR3A c-terminus
Type: COMPLEX / Details: Complex stabilized with BS3 crosslinker / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7
Details: Freshly prepared gel filtration buffer, filtered through 0.22um filter and degassed
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMImidazoleC3H4N21
2150 mMSodium ChlorideNaCl1
35 %GlycerolC3H8O31
40.5 mMTris(2-carboxyethyl)phosphineTCEP1
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was treated with BS3 crosslinker then underwent gel filtration where fractions were taken from a peak that had an elution volume consistent with formation of the complex.
Specimen supportDetails: Glow discharged using the Pelco EasiGlow. 15mA Current.
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Blot force -5, blot time 1.5 s

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9412
EM imaging opticsEnergyfilter name: TFS Selectris

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.2.1.particle selection
2SerialEMimage acquisition
4cryoSPARCv4.2.1.CTF correction
8PHENIXmodel refinement
10cryoSPARCv4.2.1initial Euler assignment
11cryoSPARCv4.2.1final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1216317
Details: Particles were picked using the cryoSPARC template picker
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135126 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00242990
ELECTRON MICROSCOPYf_angle_d0.4958160
ELECTRON MICROSCOPYf_dihedral_angle_d12.48215986
ELECTRON MICROSCOPYf_chiral_restr0.0356584
ELECTRON MICROSCOPYf_plane_restr0.0037338

+
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