8K81 | pdb_00008k81

Solution NMR Structure of ZF3 (fragment 346-396) from human Insulinoma-associated protein 1(INSM1)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into a highly flexible zinc finger module unravel INSM1 function in transcription regulation.

Zhou, H.He, X.Xiong, Y.Gong, Y.Zhang, Y.Li, S.Hu, R.Li, Y.Zhang, X.Zhou, X.Zhu, J.Yang, Y.Liu, M.

(2025) Nat Commun 16: 2162-2162

  • DOI: https://doi.org/10.1038/s41467-025-57478-2
  • Primary Citation of Related Structures:  
    8JPY, 8K81

  • PubMed Abstract: 

    Orderly development of neuroendocrine and nervous system of mammals requires INSM1, a key regulator for cell differentiation. Ectopic expression of INSM1 is closely correlated with human neuroendocrine tumorigenesis, which makes INSM1 a reliable diagnostic biomarker and potential therapeutic target. To date, INSM1 is known as a transcription repressor binding to GGGG-contained DNA element and TEAD1 using its five zinc fingers (ZFs), while the binding mechanism remains unknown. Here, we reveal highly variable conformations of the whole structure of the five ZFs, among which ZF1 adopts an unusual CCHC-fold. ZF1 binds to the TEAD domain of TEAD1 through hydrophobic interactions, and forms a ternary complex with TEAD1 and TEAD1-targeted DNA. Based on this, INSM1 cooperates with TEAD1 to repress the transcription of TEAD1-targeted genes. ZF2 and ZF3 of INSM1 can bind to DNA but have no specificity to the GGGG-contained element due to long flexible interdomain linker. Instead, INSM1 collaborates with CTCF to target genome loci having the GGGG-contained element and regulate the expression of adjacent genes. This study defines a functional mode of INSM1 by cooperating with diverse DNA-binding proteins for targeting specific genome loci in transcription regulation, and provides structural information for designing INSM1-related therapeutic drugs and diagnostic probes.


  • Organizational Affiliation
    • State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Insulinoma-associated protein 151Homo sapiensMutation(s): 0 
Gene Names: INSM1IA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q01101 (Homo sapiens)
Explore Q01101 
Go to UniProtKB:  Q01101
PHAROS:  Q01101
GTEx:  ENSG00000173404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01101
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21921004
National Natural Science Foundation of China (NSFC)China21991082

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Database references, Structure summary