PDBsum entry 3a5d

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protein Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
(+ 0 more) 561 a.a. *
(+ 0 more) 450 a.a. *
129 a.a. *
104 a.a. *
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic v1-atpase
Structure: V-type atp synthase alpha chain. Chain: a, b, c, i, j, k. Synonym: v-type atpase subunit a. V-type atp synthase beta chain. Chain: d, e, f, l, m, n. Synonym: v-type atpase subunit b. V-type atp synthase subunit d. Chain: g, o. Synonym: v-type atpase subunit d.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Strain: hb8
4.80Å     R-factor:   0.441     R-free:   0.454
Authors: N.Numoto,Y.Hasegawa,K.Takeda,K.Miki
Key ref: N.Numoto et al. (2009). Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase. EMBO Rep, 10, 1228-1234. PubMed id: 19779483
06-Aug-09     Release date:   13-Oct-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q56403  (VATA_THET8) -  V-type ATP synthase alpha chain
578 a.a.
561 a.a.
Protein chains
Pfam   ArchSchema ?
Q56404  (VATB_THET8) -  V-type ATP synthase beta chain
478 a.a.
450 a.a.
Protein chains
Pfam   ArchSchema ?
O87880  (VATD_THET8) -  V-type ATP synthase subunit D
223 a.a.
129 a.a.
Protein chains
Pfam   ArchSchema ?
P74903  (VATF_THET8) -  V-type ATP synthase subunit F
104 a.a.
104 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains A, B, C, I, J, K: 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)
+ phosphate
+ H(+)(Out)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     proton-transporting two-sector ATPase complex, catalytic domain   1 term 
  Biological process     transport   8 terms 
  Biochemical function     nucleotide binding     7 terms  


EMBO Rep 10:1228-1234 (2009)
PubMed id: 19779483  
Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase.
N.Numoto, Y.Hasegawa, K.Takeda, K.Miki.
V-type ATPases (V-ATPases) are categorized as rotary ATP synthase/ATPase complexes. The V-ATPases are distinct from F-ATPases in terms of their rotation scheme, architecture and subunit composition. However, there is no detailed structural information on V-ATPases despite the abundant biochemical and biophysical research. Here, we report a crystallographic study of V1-ATPase, from Thermus thermophilus, which is a soluble component consisting of A, B, D and F subunits. The structure at 4.5 A resolution reveals inter-subunit interactions and nucleotide binding. In particular, the structure of the central stalk composed of D and F subunits was shown to be characteristic of V1-ATPases. Small conformational changes of respective subunits and significant rearrangement of the quaternary structure observed in the three AB pairs were related to the interaction with the straight central stalk. The rotation mechanism is discussed based on a structural comparison between V1-ATPases and F1-ATPases.

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
23142977 S.Benlekbir, S.A.Bueler, and J.L.Rubinstein (2012).
Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11-Å resolution.
  Nat Struct Mol Biol, 19, 1356-1362.  
22178924 W.C.Lau, and J.L.Rubinstein (2012).
Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase.
  Nature, 481, 214-218.
PDB code: 3j0j
21278755 T.Ibuki, K.Imada, T.Minamino, T.Kato, T.Miyata, and K.Namba (2011).
Common architecture of the flagellar type III protein export apparatus and F- and V-type ATPases.
  Nat Struct Mol Biol, 18, 277-282.
PDB code: 3ajw
20173764 L.K.Lee, A.G.Stewart, M.Donohoe, R.A.Bernal, and D.Stock (2010).
The structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase.
  Nat Struct Mol Biol, 17, 373-378.
PDB code: 3k5b
20644710 P.Balabaskaran Nina, N.V.Dudkina, L.A.Kane, J.E.van Eyk, E.J.Boekema, M.W.Mather, and A.B.Vaidya (2010).
Highly divergent mitochondrial ATP synthase complexes in Tetrahymena thermophila.
  PLoS Biol, 8, e1000418.  
20838636 Z.L.Hildenbrand, S.K.Molugu, D.Stock, and R.A.Bernal (2010).
The C-H peripheral stalk base: a novel component in V1-ATPase assembly.
  PLoS One, 5, e12588.  
19834508 T.Boesen, and P.Nissen (2009).
V for victory--a V1-ATPase structure revealed.
  EMBO Rep, 10, 1211-1212.  
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.