3V3C | pdb_00003v3c

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 (Depositor), 0.331 (DCC) 
  • R-Value Work: 
    0.299 (Depositor), 0.307 (DCC) 
  • R-Value Observed: 
    0.301 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1371/journal.pone.0043045
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 111.22 kDa 
  • Atom Count: 7,578 
  • Modeled Residue Count: 1,104 
  • Deposited Residue Count: 1,106 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit c, chloroplastic
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
79Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P08212 (Pisum sativum)
Explore P08212 
Go to UniProtKB:  P08212
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08212
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



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

Query on YT3



Download:Ideal Coordinates CCD File
BA [auth G]
DA [auth H]
HA [auth K]
JA [auth L]
MA [auth N]
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
NA

Query on NA



Download:Ideal Coordinates CCD File
AA [auth F]
CA [auth G]
EA [auth H]
FA [auth I]
GA [auth J]
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.322 (Depositor), 0.331 (DCC) 
  • R-Value Work:  0.299 (Depositor), 0.307 (DCC) 
  • R-Value Observed: 0.301 (Depositor) 
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
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description