2WCR | pdb_00002wcr

Crystal Structure of Tip-Alpha N34 (HP0596) from Helicobacter pylori at pH8

• PDB DOI: https://doi.org/10.2210/pdb2WCR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-03-13 Released: 2009-05-12 
• Deposition Author(s): Tosi, T., Cioci, G., Jouravleva, K., Dian, C., Terradot, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.220 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structures of the Tumor Necrosis Factor Alpha Inducing Protein Tipalpha: A Novel Virulence Factor from Helicobacter Pylori.

Tosi, T., Cioci, G., Jouravleva, K., Dian, C., Terradot, L.

(2009) FEBS Lett 583: 1581

• PubMed: 19401200 
• DOI: https://doi.org/10.1016/j.febslet.2009.04.033
• Primary Citation Related Structures: 
  2WCQ, 2WCR


• PubMed Abstract: 
  

  Helicobacter pylori secretes a unique virulence factor, Tipalpha, that enters gastric cells and both stimulates the production of the TNF-alpha and activates the NF-kappaB pathway. The structures of a truncated version of Tipalpha (TipalphaN34) in two crystal forms are presented here. Tipalpha adopts a novel beta(1)alpha(1)alpha(2)beta(2)beta(3)alpha(3)alpha(4) topology that can be described as a combination of three domains. A first region consists in a short flexible extension, a second displays a dodecin-like fold and a third is a helical bundle domain similar to the sterile alpha motif (SAM). Analysis of the oligomerisation states of TipalphaN34 in the crystals and in solution suggests that the disulfide bridges could hold together Tipalpha monomers during their secretion in the gastric environment.

---

Organizational Affiliation: 
• European Synchrotron Radiation Facility, MX Group, Grenoble Cedex 9, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 36.59 kDa 
• Atom Count: 2,829 
• Modeled Residue Count: 295 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TNF-ALPHA INDUCER PROTEIN	A, B	159	Helicobacter pylori	Mutation(s): 0
UniProt
Find proteins for O25318 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25318  Go to UniProtKB:  O25318

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	C [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
NI	D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.220 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.88	α = 90
b = 67.26	β = 90
c = 97.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-12 
Deposition Author(s): Tosi, T., Cioci, G., Jouravleva, K., Dian, C., Terradot, L.

Revision History  

• Version 1.0: 2009-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description