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(-) Description

Title :  CRYSTAL STRUCTURE OF SUBUNIT C OF V-ATPASE
 
Authors :  M. Iwata, H. Imamura, E. Stambouli, C. Ikeda, M. Tamakoshi, K. Nagata, H. Makyio, B. Hankamer, J. Barber, M. Yoshida, K. Yokoyama, S. Iwata
Date :  14 Oct 03  (Deposition) - 13 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Alpha-Helix, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Iwata, H. Imamura, E. Stambouli, C. Ikeda, M. Tamakoshi, K. Nagata, H. Makyio, B. Hankamer, J. Barber, M. Yoshida, K. Yokoyama, S. Iwata
Crystal Structure Of A Central Stalk Subunit C And Reversible Association/Dissociation Of Vacuole-Type Atpase.
Proc. Natl. Acad. Sci. Usa V. 101 59 2004
PubMed-ID: 14684831  |  Reference-DOI: 10.1073/PNAS.0305165101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - V-TYPE ATP SYNTHASE SUBUNIT C
    Chains: A, B, C
    EC Number: 3.6.3.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3C
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: V-TYPE ATPASE SUBUNIT C

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1R5Z)

(-) Sites  (0, 0)

(no "Site" information available for 1R5Z)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:267 -A:322
2B:267 -B:322
3C:267 -C:322

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R5Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R5Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R5Z)

(-) Exons   (0, 0)

(no "Exon" information available for 1R5Z)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:320
 aligned with VATC_THET8 | P74902 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:320
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
           VATC_THET8     3 DDFAYLNARVRVRRGTLLKESFFQEALDLSFADFLRLLSETVYGGELAGQGLPDVDRAVLRTQAKLVGDLPRLVTGEAREAVRLLLLRNDLHNLQALLRAKATGRPFEEVLLLPGTLREEVWRQAYEAQDPAGMAQVLAVPGHPLARALRAVLRETQDLARVEALLAKRFFEDVAKAAKGLDQPALRDYLALEVDAENLRTAFKLQGSGLAPDAFFLKGGRFVDRVRFARLMEGDYAVLDELSGTPFSGLSGVRDLKALERGLRCVLLKEAKKGVQDPLGVGLVLAYVKEREWEAVRLRLLARRAYFGLPRAQVEEEVVC 322
               SCOP domains d1r5za_ A: V-type ATP synthase subunit C                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh........hhhhhhhhhh.hhhhhhh.....hhhhh...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r5z A   3 DDFAYLNARVRVRRGTLLKESFFQEALDLSFADFLRLLSETVYGGELAGQGLPDVDRAVLRTQAKLVGDLPRLVTGEAREAVRLLLLRNDLHNLQALLRAKATGRPFEEVLLLPGTLREEVWRQAYEAQDPAGMAQVLAVPGHPLARALRAVLRETQDLARVEALLAKRFFEDVAKAAKGLDQPALRDYLALEVDAENLRTAFKLQGSGLAPDAFFLKGGRFVDRVRFARLMEGDYAVLDELSGTPFSGLSGVRDLKALERGLRCVLLKEAKKGVQDPLGVGLVLAYVKEREWEAVRLRLLARRAYFGLPRAQVEEEVVC 322
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322


Chain B from PDB  Type:PROTEIN  Length:320
 aligned with VATC_THET8 | P74902 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:320
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
           VATC_THET8     3 DDFAYLNARVRVRRGTLLKESFFQEALDLSFADFLRLLSETVYGGELAGQGLPDVDRAVLRTQAKLVGDLPRLVTGEAREAVRLLLLRNDLHNLQALLRAKATGRPFEEVLLLPGTLREEVWRQAYEAQDPAGMAQVLAVPGHPLARALRAVLRETQDLARVEALLAKRFFEDVAKAAKGLDQPALRDYLALEVDAENLRTAFKLQGSGLAPDAFFLKGGRFVDRVRFARLMEGDYAVLDELSGTPFSGLSGVRDLKALERGLRCVLLKEAKKGVQDPLGVGLVLAYVKEREWEAVRLRLLARRAYFGLPRAQVEEEVVC 322
               SCOP domains d1r5zb_ B: V-type ATP synthase subunit C                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh........hhhhhhhhhhhhhhhhhh.....hhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r5z B   3 DDFAYLNARVRVRRGTLLKESFFQEALDLSFADFLRLLSETVYGGELAGQGLPDVDRAVLRTQAKLVGDLPRLVTGEAREAVRLLLLRNDLHNLQALLRAKATGRPFEEVLLLPGTLREEVWRQAYEAQDPAGMAQVLAVPGHPLARALRAVLRETQDLARVEALLAKRFFEDVAKAAKGLDQPALRDYLALEVDAENLRTAFKLQGSGLAPDAFFLKGGRFVDRVRFARLMEGDYAVLDELSGTPFSGLSGVRDLKALERGLRCVLLKEAKKGVQDPLGVGLVLAYVKEREWEAVRLRLLARRAYFGLPRAQVEEEVVC 322
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322


Chain C from PDB  Type:PROTEIN  Length:320
 aligned with VATC_THET8 | P74902 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:320
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
           VATC_THET8     3 DDFAYLNARVRVRRGTLLKESFFQEALDLSFADFLRLLSETVYGGELAGQGLPDVDRAVLRTQAKLVGDLPRLVTGEAREAVRLLLLRNDLHNLQALLRAKATGRPFEEVLLLPGTLREEVWRQAYEAQDPAGMAQVLAVPGHPLARALRAVLRETQDLARVEALLAKRFFEDVAKAAKGLDQPALRDYLALEVDAENLRTAFKLQGSGLAPDAFFLKGGRFVDRVRFARLMEGDYAVLDELSGTPFSGLSGVRDLKALERGLRCVLLKEAKKGVQDPLGVGLVLAYVKEREWEAVRLRLLARRAYFGLPRAQVEEEVVC 322
               SCOP domains d1r5zc_ C: V-type ATP synthase subunit C                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----vATP-synt_AC39-1r5zC01 C:7-321                                                                                                                                                                                                                                                                                             - Pfam domains (1)
           Pfam domains (2) ----vATP-synt_AC39-1r5zC02 C:7-321                                                                                                                                                                                                                                                                                             - Pfam domains (2)
           Pfam domains (3) ----vATP-synt_AC39-1r5zC03 C:7-321                                                                                                                                                                                                                                                                                             - Pfam domains (3)
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhh........hhhhhhhhhhhhhhhhhh.....hhhhh...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r5z C   3 DDFAYLNARVRVRRGTLLKESFFQEALDLSFADFLRLLSETVYGGELAGQGLPDVDRAVLRTQAKLVGDLPRLVTGEAREAVRLLLLRNDLHNLQALLRAKATGRPFEEVLLLPGTLREEVWRQAYEAQDPAGMAQVLAVPGHPLARALRAVLRETQDLARVEALLAKRFFEDVAKAAKGLDQPALRDYLALEVDAENLRTAFKLQGSGLAPDAFFLKGGRFVDRVRFARLMEGDYAVLDELSGTPFSGLSGVRDLKALERGLRCVLLKEAKKGVQDPLGVGLVLAYVKEREWEAVRLRLLARRAYFGLPRAQVEEEVVC 322
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R5Z)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: vATP-synt_AC39] (2)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (VATC_THET8 | P74902)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016820    hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances    Catalysis of the hydrolysis of an acid anhydride to directly drive the transport of a substance across a membrane.
    GO:0046933    proton-transporting ATP synthase activity, rotational mechanism    Catalysis of the transfer of protons from one side of a membrane to the other according to the reaction: ADP + H2O + phosphate + H+(in) = ATP + H+(out), by a rotational mechanism.
    GO:0046961    proton-transporting ATPase activity, rotational mechanism    Catalysis of the transfer of protons from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) = ADP + phosphate + H+(out), by a rotational mechanism.
biological process
    GO:0006754    ATP biosynthetic process    The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0042777    plasma membrane ATP synthesis coupled proton transport    The transport of protons across the plasma membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis.
    GO:0015992    proton transport    The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0033179    proton-transporting V-type ATPase, V0 domain    A protein complex that forms part of a proton-transporting V-type ATPase and mediates proton transport across a membrane. The V0 complex consists of at least four different subunits (a,c,d and e); six or more c subunits form a proton-binding rotor ring.

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  1r5z
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  3.6.3.14
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        VATC_THET8 | P74902: 1v9m 3j0j 5gar 5gas 5tsj

(-) Related Entries Specified in the PDB File

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