2R65 | pdb_00002r65

Crystal structure of Helicobacter pylori ATP dependent protease, FtsH ADP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.331 (Depositor), 0.312 (DCC) 
  • R-Value Work: 
    0.288 (Depositor), 0.269 (DCC) 
  • R-Value Observed: 
    0.290 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Structural studies on Helicobacter pyloriATP-dependent protease, FtsH

Kim, S.H.Kang, G.B.Song, H.-E.Park, S.J.Bea, M.-H.Eom, S.H.

(2008) J Synchrotron Radiat 15: 208-210

  • DOI: https://doi.org/10.1107/S090904950706846X
  • Primary Citation Related Structures: 
    2R62, 2R65

  • PubMed Abstract: 

    The ATP-dependent protease, FtsH, degrades misassembled membrane proteins for quality control like SecY, subunit a of FoF1-ATPase, and YccA, and digests short-lived soluble proteins in order to control their cellular regulation, including sigma32, LpxC and lambdacII. The FtsH protein has an N-terminal transmembrane segment and a large cytosolic region that consists of two domains, an ATPase and a protease domain. To provide a structural basis for the nucleotide-dependent domain motions and a better understanding of substrate translocation, the crystal structures of the Helicobacter pylori (Hp) FtsH ATPase domain in the nucleotide-free state and complexed with ADP, were determined. Two different structures of HpFtsH ATPase were observed, with the nucleotide-free state in an asymmetric unit, and these structures reveal the new forms and show other conformational differences between the nucleotide-free and ADP-bound state compared with previous structures. In particular, one HpFtsH Apo structure has a considerable rotation difference compared with the HpFtsH ADP complex, and this large conformational change reveals that FtsH may have the mechanical force needed for substrate translocation.


  • Organizational Affiliation
    • Department of Life Science, Cell Dynamics Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea.

Macromolecule Content 

  • Total Structure Weight: 147.68 kDa 
  • Atom Count: 9,645 
  • Modeled Residue Count: 1,245 
  • Deposited Residue Count: 1,340 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division protease ftsH homolog
A, B, C, D, E
268Helicobacter pyloriMutation(s): 1 
Gene Names: ftsH
EC: 3.4.24
UniProt
Find proteins for P71408 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P71408 
Go to UniProtKB:  P71408
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71408
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.331 (Depositor), 0.312 (DCC) 
  • R-Value Work:  0.288 (Depositor), 0.269 (DCC) 
  • R-Value Observed: 0.290 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.471α = 90
b = 219.485β = 90
c = 146.692γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description