1YCE

Structure of the rotor ring of F-type Na+-ATPase from Ilyobacter tartaricus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the rotor ring of F-Type Na+-ATPase from Ilyobacter tartaricus.

Meier, T.Polzer, P.Diederichs, K.Welte, W.Dimroth, P.

(2005) Science 308: 659-662

  • DOI: 10.1126/science.1111199
  • Primary Citation of Related Structures:  
    1YCE

  • PubMed Abstract: 
  • In the crystal structure of the membrane-embedded rotor ring of the sodium ion-translocating adenosine 5'-triphosphate (ATP) synthase of Ilyobacter tartaricus at 2.4 angstrom resolution, 11 c subunits are assembled into an hourglass-shaped cylinder with 11-fold symmetry ...

    In the crystal structure of the membrane-embedded rotor ring of the sodium ion-translocating adenosine 5'-triphosphate (ATP) synthase of Ilyobacter tartaricus at 2.4 angstrom resolution, 11 c subunits are assembled into an hourglass-shaped cylinder with 11-fold symmetry. Sodium ions are bound in a locked conformation close to the outer surface of the cylinder near the middle of the membrane. The structure supports an ion-translocation mechanism in the intact ATP synthase in which the binding site converts from the locked conformation into one that opens toward subunit a as the rotor ring moves through the subunit a/c interface.


    Organizational Affiliation

    Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH), Zürich Hönggerberg, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
subunit c
A, B, C, D, E, F, G, H
89Ilyobacter tartaricusMutation(s): 0 
Gene Names: atpE
Membrane Entity: Yes 
UniProt
Find proteins for Q8KRV3 (Ilyobacter tartaricus)
Explore Q8KRV3 
Go to UniProtKB:  Q8KRV3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F09
Query on F09

Download Ideal Coordinates CCD File 
BB [auth E] , BC [auth R] , BD [auth i] , BE [auth v] , DB [auth F] , DC [auth S] , DD [auth j] , FB [auth G] , 
BB [auth E], BC [auth R], BD [auth i], BE [auth v], DB [auth F], DC [auth S], DD [auth j], FB [auth G], FC [auth T], FD [auth k], HB [auth H], HC [auth U], HD [auth l], JB [auth I], JC [auth V], JD [auth m], LB [auth J], LC [auth a], LD [auth n], NB [auth K], NC [auth b], ND [auth o], PB [auth L], PC [auth c], PD [auth p], RB [auth M], RC [auth d], RD [auth q], TA [auth A], TB [auth N], TC [auth e], TD [auth r], VA [auth B], VB [auth O], VC [auth f], VD [auth s], XA [auth C], XB [auth P], XC [auth g], XD [auth t], ZA [auth D], ZB [auth Q], ZC [auth h], ZD [auth u]
NONAN-1-OL
C9 H20 O
ZWRUINPWMLAQRD-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
AB [auth E] , AC [auth R] , AD [auth i] , AE [auth v] , CB [auth F] , CC [auth S] , CD [auth j] , EB [auth G] , 
AB [auth E], AC [auth R], AD [auth i], AE [auth v], CB [auth F], CC [auth S], CD [auth j], EB [auth G], EC [auth T], ED [auth k], GB [auth H], GC [auth U], GD [auth l], IB [auth I], IC [auth V], ID [auth m], KB [auth J], KC [auth a], KD [auth n], MB [auth K], MC [auth b], MD [auth o], OB [auth L], OC [auth c], OD [auth p], QB [auth M], QC [auth d], QD [auth q], SA [auth A], SB [auth N], SC [auth e], SD [auth r], UA [auth B], UB [auth O], UC [auth f], UD [auth s], WA [auth C], WB [auth P], WC [auth g], WD [auth t], YA [auth D], YB [auth Q], YC [auth h], YD [auth u]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.7α = 90
b = 140β = 118.4
c = 153γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance