3NA7 | pdb_00003na7

2.2 Angstrom Structure of the HP0958 Protein from Helicobacter pylori CCUG 17874

• PDB DOI: https://doi.org/10.2210/pdb3NA7/pdb

• Classification: Gene Regulation, Chaperone
• Organism(s): Helicobacter pylori NCTC 11638
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-01 Released: 2010-09-22 
• Deposition Author(s): Caly, D.L., O'Toole, P.W., Moore, S.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.294 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Literature

The 2.2-A Structure of the HP0958 Protein from Helicobacter pylori Reveals a Kinked Anti-Parallel Coiled-Coil Hairpin Domain and a Highly Conserved Zn-Ribbon Domain

Caly, D.L., O'Toole, P.W., Moore, S.A.

(2010) J Mol Biology 403: 405-419

• PubMed: 20826163 
• DOI: https://doi.org/10.1016/j.jmb.2010.08.051
• Primary Citation of Related Structures:  
  3NA7


• PubMed Abstract: 
  

  We have determined the 2.2-Å structure of the HP0958 protein from the human gastric pathogen Helicobacter pylori. HP0958 is essential for flagellum formation and motility. It functions as a chaperone for RpoN (σ(54)) and also controls the stability and translation of mRNA for the major flagellin subunit FlaA. The protein is composed of a highly elongated and kinked coiled-coil hairpin domain (residues 1-170), followed by a C(4) Zn-ribbon domain (residues 174-238). The Zn-ribbon domain is rich in aromatic and positively charged amino acid residues. Electrophoretic mobility shift assays identified residues in a positively charged region of the Zn-ribbon domain of HP0958 whose mutation alters the mobility of an HP0958-flaA mRNA complex. Mutation of surface residues in the coiled-coil domain did not result in an observable change in the mobility of the HP0958-flaA transcript complex. The data thus suggest the arrangement of HP0958 into distinct structural and functional domains.

---

Organizational Affiliation: 

Department of Microbiology, University College Cork, Cork, Ireland.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 30.13 kDa 
• Atom Count: 1,994 
• Modelled Residue Count: 237 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HP0958	A	256	Helicobacter pylori NCTC 11638	Mutation(s): 0  Gene Names: HP0958

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.294 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.72	α = 90
b = 37.951	β = 110.66
c = 66.056	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Caly, D.L., O'Toole, P.W., Moore, S.A.

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations