3F4M | pdb_00003f4m

Crystal structure of TIPE2

• PDB DOI: https://doi.org/10.2210/pdb3F4M/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-01 Released: 2009-03-17 
• Deposition Author(s): Zhang, X., Wang, J., Shi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.243 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal structure of TIPE2 provides insights into immune homeostasis

Zhang, X., Wang, J., Fan, C., Li, H., Sun, H., Gong, S., Chen, Y.H., Shi, Y.

(2009) Nat Struct Mol Biol 16: 89-90

• PubMed: 19079267 
• DOI: https://doi.org/10.1038/nsmb.1522
• Primary Citation Related Structures: 
  3F4M


• PubMed Abstract: 
  

  TNFAIP8-like 2 (TIPE2) has an essential role in immune homeostasis, yet the underlying mechanism remains enigmatic. The high-resolution crystal structure of TIPE2 reveals a previously uncharacterized fold that is different from the predicted fold of a death effector domain (DED). Strikingly, TIPE2 contains a large, hydrophobic central cavity that is poised for cofactor binding. These structural features will be important for understanding the functions of TIPE2 and other TNFAIP8 family proteins.

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Organizational Affiliation: 
• Center for Structural Biology and Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.15 kDa 
• Atom Count: 1,328 
• Modeled Residue Count: 154 
• Deposited Residue Count: 161 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor, alpha-induced protein 8-like protein 2	A	161	Homo sapiens	Mutation(s): 0  Gene Names: TNFAIP8L2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P589 (Homo sapiens) Explore Q6P589  Go to UniProtKB:  Q6P589
PHAROS:  Q6P589 GTEx:  ENSG00000163154

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.243 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.815	α = 90
b = 91.815	β = 90
c = 67.952	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Zhang, X., Wang, J., Shi, Y.

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations