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,
89Ilyobacter tartaricusMutation(s): 0 
Gene Names: atpE
Membrane Entity: Yes 
UniProt
Find proteins for Q8KRV3 (Ilyobacter tartaricus)
Explore Q8KRV3 
Go to UniProtKB:  Q8KRV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KRV3
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],
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],
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