9BAX | pdb_00009bax

PI4KA complex bound to C-terminus of EFR3A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for plasma membrane recruitment of PI4KA by EFR3.

Suresh, S.Shaw, A.L.Pemberton, J.G.Scott, M.K.Harris, N.J.Parson, M.A.H.Jenkins, M.L.Rohilla, P.Alvarez-Prats, A.Balla, T.Yip, C.K.Burke, J.E.

(2024) Sci Adv 10: eadp6660-eadp6660

  • DOI: https://doi.org/10.1126/sciadv.adp6660
  • Primary Citation of Related Structures:  
    9BAX

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein EFR3 homolog AA [auth C],
E [auth H]
130Homo sapiensMutation(s): 0 
Gene Names: EFR3AKIAA0143
UniProt & NIH Common Fund Data Resources
Find proteins for Q14156 (Homo sapiens)
Explore Q14156 
Go to UniProtKB:  Q14156
PHAROS:  Q14156
GTEx:  ENSG00000132294 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14156
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4-kinase alphaB,
F [auth A]
2,102Homo sapiensMutation(s): 0 
Gene Names: PI4KAPIK4PIK4CA
EC: 2.7.1.67
UniProt & NIH Common Fund Data Resources
Find proteins for P42356 (Homo sapiens)
Explore P42356 
Go to UniProtKB:  P42356
PHAROS:  P42356
GTEx:  ENSG00000241973 
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UniProt GroupP42356
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tetratricopeptide repeat protein 7BC [auth F],
G [auth D]
843Homo sapiensMutation(s): 0 
Gene Names: TTC7BTTC7L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86TV6 (Homo sapiens)
Explore Q86TV6 
Go to UniProtKB:  Q86TV6
PHAROS:  Q86TV6
GTEx:  ENSG00000165914 
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UniProt GroupQ86TV6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HyccinD [auth G],
H [auth E]
308Homo sapiensMutation(s): 0 
Gene Names: HYCC1DRCTNNB1AFAM126A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYI3 (Homo sapiens)
Explore Q9BYI3 
Go to UniProtKB:  Q9BYI3
PHAROS:  Q9BYI3
GTEx:  ENSG00000122591 
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UniProt GroupQ9BYI3
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaNSERC-2020-04241
Canadian Institutes of Health Research (CIHR)CanadaPJT-168907
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2018-03951
Canadian Institutes of Health Research (CIHR)CanadaPJT-195808

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-21
    Changes: Data collection