7F09

Crystal structure of the HLH-Lz domain of human TFE3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the dimerization mechanism of human transcription factor E3.

Yang, G.Li, P.Liu, Z.Wu, S.Zhuang, C.Qiao, H.Zheng, L.Fang, P.Lei, C.Wang, J.

(2021) Biochem Biophys Res Commun 569: 41-46

  • DOI: https://doi.org/10.1016/j.bbrc.2021.06.091
  • Primary Citation of Related Structures:  
    7F09

  • PubMed Abstract: 

    The transcription factor for immunoglobulin heavy-chain enhancer 3 (TFE3) is a member of the microphthalmia (MiT/TFE) transcription factor family. Dysregulation of TFE3 due to chromosomal abnormalities is associated with a subset of human renal cell carcinoma. Little structural information of this key transcription factor has been reported. In this study, we determined the crystal structure of the helix-loop-helix leucine zipper (HLH-Lz) domain of human TFE3 to a resolution of 2.6 Å. The HLH-Lz domain is critical for the dimerization and function of TFE3. Our structure showed that the conserved HLH region formed a four-helix bundle structure with a predominantly hydrophobic core, and the leucine zipper region contributed to the function of TFE3 by promoting dimer interaction and providing partner selectivity. Together, our results elucidated the dimerization mechanism of this important transcription factor, providing the structural basis for the development of inhibiting strategies for treating TFE3 dysregulated diseases.


  • Organizational Affiliation

    Center for Supramolecular Chemistry and Catalysis and Department of Chemistry, College of Sciences, Shanghai University, 99 Shang-Da Road, Shanghai, 200444, China; State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor E3
A, B, C, D
74Homo sapiensMutation(s): 0 
Gene Names: TFE3BHLHE33
UniProt & NIH Common Fund Data Resources
Find proteins for P19532 (Homo sapiens)
Explore P19532 
Go to UniProtKB:  P19532
PHAROS:  P19532
GTEx:  ENSG00000068323 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19532
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth B]
G [auth B]
H [auth B]
K [auth C]
L [auth C]
F [auth B],
G [auth B],
H [auth B],
K [auth C],
L [auth C],
M [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
I [auth B]
J [auth B]
N [auth D]
O [auth D]
E [auth A],
I [auth B],
J [auth B],
N [auth D],
O [auth D],
P [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.94α = 85.24
b = 47.37β = 87.21
c = 69.96γ = 88.32
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21977107
National Natural Science Foundation of China (NSFC)China21977108
National Natural Science Foundation of China (NSFC)China21778067
National Natural Science Foundation of China (NSFC)China21778064

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description