9N1S | pdb_00009n1s

Crystal structure of the Transport and Golgi Organization protein 2 Homolog (TANGO2) tetragonal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.245 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of Human Transport and Golgi Organization 2 Homolog (TANGO2) Protein Reveals an alpha beta beta alpha-Fold Arrangement.

Cooper, A.Powers, A.Battaile, K.P.Mohsen, A.W.Johnson, D.K.Lovell, S.Ghaloul-Gonzalez, L.

(2026) Proteins 94: 515-528

  • DOI: https://doi.org/10.1002/prot.70023
  • Primary Citation Related Structures: 
    9BWA, 9N1S

  • PubMed Abstract: 

    Transport and Golgi Organization 2 Homolog (TANGO2) protein deficiency disorder (TDD) is a rare autosomal recessive disorder characterized by multi-systemic abnormalities and significant phenotypic variability including neurodevelopmental delay, seizures, intermittent ataxia, hypothyroidism, rhabdomyolysis, life-threatening metabolic derangements, and cardiac arrhythmias. Mutations in TANGO2 result in mitochondrial dysfunction, abnormal lipid homeostasis with cardiolipin deficiency, and impaired Golgi-ER trafficking in TANGO2 patient-derived cells. Despite the wide recognition of the clinical manifestations of TDD and numerous molecular studies, the precise function of TANGO2 and the pathophysiology of TDD remain poorly understood. A computationally derived three-dimensional structure model suggested that TANGO2 adopts an αββα-fold, similar to the N-terminal nucleophile aminohydrolase (Ntn) superfamily of proteins, but the experimentally verified structure has not been available thus far. Here, we present the first crystal structure of the recombinant human TANGO2, determined at 1.70 Å resolution. The X-ray structure data confirmed its predicted tertiary fold with similarity to the Ntn-hydrolase family of proteins, and the comparative analysis of the active site architecture, including residues involved in catalysis and putative ligand binding site, suggests a potential hydrolase function. Additional examination of the common mutation sites found in TDD patients provides insight regarding their potential effect on protein structure integrity.


  • Organizational Affiliation
    • Protein Structure and X-Ray Crystallography Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas, USA.

Macromolecule Content 

  • Total Structure Weight: 31.98 kDa 
  • Atom Count: 2,205 
  • Modeled Residue Count: 274 
  • Deposited Residue Count: 282 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transport and Golgi organization protein 2 homolog282Homo sapiensMutation(s): 0 
Gene Names: TANGO2C22orf25
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ICL3 (Homo sapiens)
Explore Q6ICL3 
Go to UniProtKB:  Q6ICL3
PHAROS:  Q6ICL3
GTEx:  ENSG00000183597 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ICL3
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.245 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.895α = 90
b = 49.895β = 90
c = 241.716γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesS10OD030394

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references
  • Version 1.2: 2026-01-14
    Changes: Database references