9C6T | pdb_00009c6t

Structure of the Human ISM1 TSR-AMOP domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 
    0.366 (Depositor), 0.348 (DCC) 
  • R-Value Work: 
    0.332 (Depositor), 0.334 (DCC) 
  • R-Value Observed: 
    0.333 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling.

Li, T.Stayrook, S.E.Li, W.Wang, Y.Li, H.Zhang, J.Liu, Y.Klein, D.E.

(2025) Nat Commun 16: 3580-3580

  • DOI: https://doi.org/10.1038/s41467-025-58828-w
  • Primary Citation of Related Structures:  
    9C6T

  • PubMed Abstract: 

    Isthmin-1 (ISM1) is a recently described adipokine with insulin-like properties that can control hyperglycemia and liver steatosis. Additionally, ISM1 is proposed to play critical roles in patterning, angiogenesis, vascular permeability, and apoptosis. A key feature of ISM1 is its AMOP (adhesion-associated domain in MUC4 (Mucin-4) and other proteins) domain which is essential for many of its functions. However, the molecular details of AMOP domains remain elusive as there are no descriptions of their structure. Here we determined the crystal structure of ISM1 including its thrombospondin type I repeat (TSR) and AMOP domain. Interestingly, ISM1's AMOP domain exhibits a distinct fold with similarities to bacterial streptavidin. When comparing our structure to predicted structures of other AMOP domains, we observed that while the core streptavidin-like barrel is conserved, the surface helices and loops vary greatly. Thus, the AMOP domain fold allows for structural plasticity that may underpin its diverse functions. Furthermore, and contrary to prior studies, we show that highly purified ISM1 does not stimulate AKT phosphorylation on 3T3-F442A pre-adipocytes. Rather, we find that co-purifying growth factors are responsible for this activity. Together, our data reveal the structure and clarify functional studies of this enigmatic protein.


  • Organizational Affiliation
    • Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isthmin-1
A, B
247Homo sapiensMutation(s): 0 
Gene Names: ISM1C20orf82ISM
UniProt & NIH Common Fund Data Resources
Find proteins for B1AKI9 (Homo sapiens)
Explore B1AKI9 
Go to UniProtKB:  B1AKI9
PHAROS:  B1AKI9
GTEx:  ENSG00000101230 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1AKI9
Glycosylation
Glycosylation Sites: 2Go to GlyGen: B1AKI9-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free:  0.366 (Depositor), 0.348 (DCC) 
  • R-Value Work:  0.332 (Depositor), 0.334 (DCC) 
  • R-Value Observed: 0.333 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.255α = 90
b = 114.255β = 90
c = 168.221γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Database references