3V3C

Crystal Structure of Chloroplast ATP synthase c-ring from Pisum sativum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.301 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure and flexibility of the C-ring in the electromotor of rotary F(o)F(1)-ATPase of pea chloroplasts.

Saroussi, S.Schushan, M.Ben-Tal, N.Junge, W.Nelson, N.

(2012) PLoS One 7: e43045-e43045

  • DOI: 10.1371/journal.pone.0043045
  • Primary Citation of Related Structures:  
    3V3C

  • PubMed Abstract: 
  • A ring of 8-15 identical c-subunits is essential for ion-translocation by the rotary electromotor of the ubiquitous F(O)F(1)-ATPase. Here we present the crystal structure at 3.4Å resolution of the c-ring from chloroplasts of a higher plant (Pisum sativum), determined using a native preparation ...

    A ring of 8-15 identical c-subunits is essential for ion-translocation by the rotary electromotor of the ubiquitous F(O)F(1)-ATPase. Here we present the crystal structure at 3.4Å resolution of the c-ring from chloroplasts of a higher plant (Pisum sativum), determined using a native preparation. The crystal structure was found to resemble that of an (ancestral) cyanobacterium. Using elastic network modeling to investigate the ring's eigen-modes, we found five dominant modes of motion that fell into three classes. They revealed the following deformations of the ring: (I) ellipsoidal, (II) opposite twisting of the luminal circular surface of the ring against the stromal surface, and (III) kinking of the hairpin-shaped monomers in the middle, resulting in bending/stretching of the ring. Extension of the elastic network analysis to rings of different c(n)-symmetry revealed the same classes of dominant modes as in P. sativum (c(14)). We suggest the following functional roles for these classes: The first and third classes of modes affect the interaction of the c-ring with its counterparts in F(O), namely subunits a and bb'. These modes are likely to be involved in ion-translocation and torque generation. The second class of deformation, along with deformations of subunits γ and ε might serve to elastically buffer the torque transmission between F(O) and F(1).


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit c, chloroplastic
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M, N
79Pisum sativumMutation(s): 0 
Gene Names: atpH
Membrane Entity: Yes 
UniProt
Find proteins for P08212 (Pisum sativum)
Explore P08212 
Go to UniProtKB:  P08212
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

Download Ideal Coordinates CCD File 
O [auth A]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
YT3
Query on YT3

Download Ideal Coordinates CCD File 
BA [auth G] , DA [auth H] , HA [auth K] , JA [auth L] , MA [auth N] , P [auth A] , T [auth C] , U [auth D] , 
BA [auth G], DA [auth H], HA [auth K], JA [auth L], MA [auth N], P [auth A], T [auth C], U [auth D], W [auth E], Z [auth F]
YTTRIUM (III) ION
Y
GRTBAGCGDOYUBE-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth F] , CA [auth G] , EA [auth H] , FA [auth I] , GA [auth J] , IA [auth K] , KA [auth L] , LA [auth M] , 
AA [auth F], CA [auth G], EA [auth H], FA [auth I], GA [auth J], IA [auth K], KA [auth L], LA [auth M], Q [auth A], R [auth A], S [auth B], V [auth D], X [auth E], Y [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.301 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.13α = 90
b = 102.38β = 101.22
c = 122.43γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references