PDBsum entry 2jdi

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
487 a.a. *
467 a.a. *
184 a.a. *
88 a.a. *
25 a.a. *
ANP ×5
_MG ×5
Waters ×2322
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Ground state structure of f1-atpase from bovine heart mitochondria (bovine f1-atpase crystallised in the absence of azide)
Structure: Atp synthase subunit alpha heart isoform. Chain: a, b, c. Fragment: residues 44-553. Synonym: atp synthase alpha chain heart isoform. Atp synthase subunit beta. Chain: d, e, f. Fragment: residues 47-528. Synonym: atp synthase beta chain. Atp synthase gamma chain.
Source: Bos taurus. Bovine. Organism_taxid: 9913. Organ: heart. Tissue: muscle. Organelle: mitochondria. Other_details: mitochondria. Organelle: mitochondria
1.90Å     R-factor:   0.177     R-free:   0.220
Authors: M.W.Bowler,M.G.Montgomery,A.G.W.Leslie,J.E.Walker
Key ref:
M.W.Bowler et al. (2007). Ground state structure of F1-ATPase from bovine heart mitochondria at 1.9 A resolution. J Biol Chem, 282, 14238-14242. PubMed id: 17350959 DOI: 10.1074/jbc.M700203200
09-Jan-07     Release date:   13-Mar-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P19483  (ATPA_BOVIN) -  ATP synthase subunit alpha, mitochondrial
553 a.a.
487 a.a.*
Protein chains
Pfam   ArchSchema ?
P00829  (ATPB_BOVIN) -  ATP synthase subunit beta, mitochondrial
528 a.a.
467 a.a.
Protein chain
Pfam   ArchSchema ?
P05631  (ATPG_BOVIN) -  ATP synthase subunit gamma, mitochondrial
298 a.a.
184 a.a.
Protein chain
Pfam   ArchSchema ?
P05630  (ATPD_BOVIN) -  ATP synthase subunit delta, mitochondrial
168 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P05632  (ATP5E_BOVIN) -  ATP synthase subunit epsilon, mitochondrial
51 a.a.
25 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains D, E, F: E.C.  - H(+)-transporting two-sector ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + H+(In) = ADP + phosphate + H+(Out)
+ H(2)O
+ H(+)(In)
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity
+ phosphate
+ H(+)(Out)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   13 terms 
  Biological process     transport   12 terms 
  Biochemical function     nucleotide binding     10 terms  


DOI no: 10.1074/jbc.M700203200 J Biol Chem 282:14238-14242 (2007)
PubMed id: 17350959  
Ground state structure of F1-ATPase from bovine heart mitochondria at 1.9 A resolution.
M.W.Bowler, M.G.Montgomery, A.G.Leslie, J.E.Walker.
The structure of bovine F(1)-ATPase, crystallized in the presence of AMP-PNP and ADP, but in the absence of azide, has been determined at 1.9A resolution. This structure has been compared with the previously described structure of bovine F(1)-ATPase determined at 1.95A resolution with crystals grown under the same conditions but in the presence of azide. The two structures are extremely similar, but they differ in the nucleotides that are bound to the catalytic site in the beta(DP)-subunit. In the present structure, the nucleotide binding sites in the beta(DP)- and beta(TP)-subunits are both occupied by AMP-PNP, whereas in the earlier structure, the beta(TP) site was occupied by AMP-PNP and the beta(DP) site by ADP, where its binding is enhanced by a bound azide ion. Also, the conformation of the side chain of the catalytically important residue, alphaArg-373 differs in the beta(DP)- and beta(TP)-subunits. Thus, the structure with bound azide represents the ADP inhibited state of the enzyme, and the new structure represents a ground state intermediate in the active catalytic cycle of ATP hydrolysis.
  Selected figure(s)  
Figure 1.
FIGURE 1. The [DP] binding site in the structure of the azide-free F[1]-ATPase from bovine heart mitochondria. The view is in stereo. The difference electron density (F[o] - F[c]) for the -phosphate, contoured at 3 before its inclusion in the model, is shown as a green mesh. The 2F[o] - F[c] densities for ADP and Arg-373 are shown as a blue mesh contoured at 1.5 . The red and green spheres represent the catalytic water molecule and a magnesium ion, respectively.
Figure 2.
FIGURE 2. Comparison of the catalytic sites in the [DP]-subunits of the azide-free F[1]-ATPase and N[3]^--F[1] structures. The view (in stereo) was made by superimposing the P-loops of the two structures. The catalytic site in the azide-free structure is in color, and that in the N^-[3]-F[1] structure is gray.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 14238-14242) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23334411 S.Arai, S.Saijo, K.Suzuki, K.Mizutani, Y.Kakinuma, Y.Ishizuka-Katsura, N.Ohsawa, T.Terada, M.Shirouzu, S.Yokoyama, S.Iwata, I.Yamato, and T.Murata (2013).
Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures.
  Nature, 493, 703-707.
PDB codes: 3vr2 3vr3 3vr4 3vr5 3vr6
21602818 G.Cingolani, and T.M.Duncan (2011).
Structure of the ATP synthase catalytic complex (F(1)) from Escherichia coli in an autoinhibited conformation.
  Nat Struct Mol Biol, 18, 701-707.  
21481781 K.Okazaki, and S.Takada (2011).
Structural Comparison of F(1)-ATPase: Interplay among Enzyme Structures, Catalysis, and Rotations.
  Structure, 19, 588-598.  
21383131 T.Beke-Somfai, P.Lincoln, and B.Nordén (2011).
Double-lock ratchet mechanism revealing the role of alphaSER-344 in FoF1 ATP synthase.
  Proc Natl Acad Sci U S A, 108, 4828-4833.  
20847295 I.N.Watt, M.G.Montgomery, M.J.Runswick, A.G.Leslie, and J.E.Walker (2010).
Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria.
  Proc Natl Acad Sci U S A, 107, 16823-16827.
PDB code: 2xnd
20693684 M.W.Bowler, M.Guijarro, S.Petitdemange, I.Baker, O.Svensson, M.Burghammer, C.Mueller-Dieckmann, E.J.Gordon, D.Flot, S.M.McSweeney, and G.A.Leonard (2010).
Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection.
  Acta Crystallogr D Biol Crystallogr, 66, 855-864.  
20371322 R.Shimo-Kon, E.Muneyuki, H.Sakai, K.Adachi, M.Yoshida, and K.Kinosita (2010).
Chemo-mechanical coupling in F(1)-ATPase revealed by catalytic site occupancy during catalysis.
  Biophys J, 98, 1227-1236.  
20336770 Y.Ito, and M.Ikeguchi (2010).
Structural fluctuation and concerted motions in F(1)-ATPase: A molecular dynamics study.
  J Comput Chem, 31, 2175-2185.  
19995987 D.M.Rees, A.G.Leslie, and J.E.Walker (2009).
The structure of the membrane extrinsic region of bovine ATP synthase.
  Proc Natl Acad Sci U S A, 106, 21597-21601.
PDB code: 2wss
19878046 D.Sengupta, A.Rampioni, and S.J.Marrink (2009).
Simulations of the c-subunit of ATP-synthase reveal helix rearrangements.
  Mol Membr Biol, 26, 422-434.  
19966409 J.Sanchez-Weatherby, M.W.Bowler, J.Huet, A.Gobbo, F.Felisaz, B.Lavault, R.Moya, J.Kadlec, R.B.Ravelli, and F.Cipriani (2009).
Improving diffraction by humidity control: a novel device compatible with X-ray beamlines.
  Acta Crystallogr D Biol Crystallogr, 65, 1237-1246.
PDB codes: 2w6e 2w6f 2w6g 2w6h 2w6i 2w6j
19362069 L.Bae, and S.B.Vik (2009).
A more robust version of the Arginine 210-switched mutant in subunit a of the Escherichia coli ATP synthase.
  Biochim Biophys Acta, 1787, 1129-1134.  
19502237 M.Sekiya, R.K.Nakamoto, M.K.Al-Shawi, M.Nakanishi-Matsui, and M.Futai (2009).
Temperature dependence of single molecule rotation of the Escherichia coli ATP synthase F1 sector reveals the importance of gamma-beta subunit interactions in the catalytic dwell.
  J Biol Chem, 284, 22401-22410.  
19423706 M.Vollmar, D.Schlieper, M.Winn, C.Büchner, and G.Groth (2009).
Structure of the c14 rotor ring of the proton translocating chloroplast ATP synthase.
  J Biol Chem, 284, 18228-18235.
PDB code: 2w5j
19246448 N.Mnatsakanyan, A.M.Krishnakumar, T.Suzuki, and J.Weber (2009).
The role of the betaDELSEED-loop of ATP synthase.
  J Biol Chem, 284, 11336-11345.  
19636076 N.Mnatsakanyan, J.A.Hook, L.Quisenberry, and J.Weber (2009).
ATP synthase with its gamma subunit reduced to the N-terminal helix can still catalyze ATP synthesis.
  J Biol Chem, 284, 26519-26525.  
19801635 V.Giorgio, E.Bisetto, M.E.Soriano, F.Dabbeni-Sala, E.Basso, V.Petronilli, M.A.Forte, P.Bernardi, and G.Lippe (2009).
Cyclophilin D modulates mitochondrial F0F1-ATP synthase by interacting with the lateral stalk of the complex.
  J Biol Chem, 284, 33982-33988.  
19233840 V.Kabaleeswaran, H.Shen, J.Symersky, J.E.Walker, A.G.Leslie, and D.M.Mueller (2009).
Asymmetric structure of the yeast F1 ATPase in the absence of bound nucleotides.
  J Biol Chem, 284, 10546-10551.
PDB code: 3fks
19458712 W.Junge, H.Sielaff, and S.Engelbrecht (2009).
Torque generation and elastic power transmission in the rotary F(O)F(1)-ATPase.
  Nature, 459, 364-370.  
18846414 A.F.Lodeyro, M.V.Castelli, and O.A.Roveri (2008).
ATP hydrolysis-driven H(+) translocation is stimulated by sulfate, a strong inhibitor of mitochondrial ATP synthesis.
  J Bioenerg Biomembr, 40, 269-279.  
18434546 C.Kötting, A.Kallenbach, Y.Suveyzdis, A.Wittinghofer, and K.Gerwert (2008).
The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy.
  Proc Natl Acad Sci U S A, 105, 6260-6265.  
18573072 C.von Ballmoos, G.M.Cook, and P.Dimroth (2008).
Unique rotary ATP synthase and its biological diversity.
  Annu Rev Biophys, 37, 43-64.  
19075235 D.Okuno, R.Fujisawa, R.Iino, Y.Hirono-Hara, H.Imamura, and H.Noji (2008).
Correlation between the conformational states of F1-ATPase as determined from its crystal structure and single-molecule rotation.
  Proc Natl Acad Sci U S A, 105, 20722-20727.  
18721138 D.Pogoryelov, Y.Nikolaev, U.Schlattner, K.Pervushin, P.Dimroth, and T.Meier (2008).
Probing the rotor subunit interface of the ATP synthase from Ilyobacter tartaricus.
  FEBS J, 275, 4850-4862.  
18958608 E.Bisetto, P.Picotti, V.Giorgio, V.Alverdi, I.Mavelli, and G.Lippe (2008).
Functional and stoichiometric analysis of subunit e in bovine heart mitochondrial F(0)F(1)ATP synthase.
  J Bioenerg Biomembr, 40, 257-267.  
18723591 H.Sielaff, H.Rennekamp, S.Engelbrecht, and W.Junge (2008).
Functional halt positions of rotary FOF1-ATPase correlated with crystal structures.
  Biophys J, 95, 4979-4987.  
18579516 H.Z.Mao, C.G.Abraham, A.M.Krishnakumar, and J.Weber (2008).
A functionally important hydrogen-bonding network at the betaDP/alphaDP interface of ATP synthase.
  J Biol Chem, 283, 24781-24788.  
18216260 J.Pu, and M.Karplus (2008).
How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase.
  Proc Natl Acad Sci U S A, 105, 1192-1197.  
18515057 R.K.Nakamoto, J.A.Baylis Scanlon, and M.K.Al-Shawi (2008).
The rotary mechanism of the ATP synthase.
  Arch Biochem Biophys, 476, 43-50.  
18064048 R.Watanabe, R.Iino, K.Shimabukuro, M.Yoshida, and H.Noji (2008).
Temperature-sensitive reaction intermediate of F(1)-ATPase.
  EMBO Rep, 9, 84-90.  
19011636 T.Masaike, F.Koyama-Horibe, K.Oiwa, M.Yoshida, and T.Nishizaka (2008).
Cooperative three-step motions in catalytic subunits of F(1)-ATPase correlate with 80 degrees and 40 degrees substep rotations.
  Nat Struct Mol Biol, 15, 1326-1333.  
18003896 H.Z.Mao, and J.Weber (2007).
Identification of the betaTP site in the x-ray structure of F1-ATPase as the high-affinity catalytic site.
  Proc Natl Acad Sci U S A, 104, 18478-18483.  
17698806 J.R.Gledhill, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2007).
Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols.
  Proc Natl Acad Sci U S A, 104, 13632-13637.
PDB codes: 2jiz 2jj1 2jj2
17895376 J.R.Gledhill, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2007).
How the regulatory protein, IF(1), inhibits F(1)-ATPase from bovine mitochondria.
  Proc Natl Acad Sci U S A, 104, 15671-15676.
PDB code: 2v7q
17721548 T.Ariga, E.Muneyuki, and M.Yoshida (2007).
F1-ATPase rotates by an asymmetric, sequential mechanism using all three catalytic subunits.
  Nat Struct Mol Biol, 14, 841-846.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.