3J9V Hydrolase date Feb 23, 2015
title Yeast V-Atpase State 3
authors J.Zhao, S.Benlekbir, J.L.Rubinstein
compound source
Molecule: V-Type Proton Atpase Subunit A, Vacuolar Isoform
Chain: b
Synonym: V-Atpase A 1 Subunit, V-Atpase 95 Kda Subunit, Vac Protein 1, Vacuolar Proton Pump A Subunit, Vacuolar Proton Translocating Atpase Subunit A 1;
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Strain: Saby31

Molecule: V-Type Proton Atpase Subunit C
Chain: O
Synonym: V-Atpase Subunit C, V-Atpase 42 Kda Subunit, Vacuo Pump Subunit C;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Strain: Saby31

Molecule: V-Type Proton Atpase Subunit D
Chain: M
Synonym: V-Atpase Subunit D, Vacuolar Proton Pump Subunit D
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Strain: Saby31

Molecule: V-Type Proton Atpase Subunit F
Chain: N
Synonym: V-Atpase Subunit F, V-Atpase 14 Kda Subunit, Vacuo Pump Subunit F;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Strain: Saby31

Molecule: V-Type Proton Atpase Catalytic Subunit A
Chain: E, A, C
Fragment: See Remark 999
Synonym: V-Atpase Subunit A, Vacuolar Proton Pump Subunit A Endonuclease Pi-Scei, Sce Vma Intein, Vma1-Derived Endonucl
Ec: 3.6.3.14, 3.1.-.-
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Strain: Saby31

Molecule: V-Type Proton Atpase Subunit B
Chain: F, B, D
Synonym: V-Atpase Subunit B, V-Atpase 57 Kda Subunit, Vacuo Pump Subunit B;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Strain: Saby31

Molecule: V-Type Proton Atpase Subunit D
Chain: Q
Synonym: V-Atpase Subunit D, V-Atpase 39 Kda Subunit, V-Atp Subunit M39, Vacuolar Proton Pump Subunit D;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Strain: Saby31

Molecule: V-Type Proton Atpase Subunit G
Chain: J, L, H
Synonym: V-Atpase Subunit G, V-Atpase 13 Kda Subunit, Vacuo Pump Subunit G;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Strain: Saby31

Molecule: V-Type Proton Atpase Subunit E
Chain: I, K, G
Synonym: V-Atpase Subunit E, V-Atpase 27 Kda Subunit, Vacuo Pump Subunit E;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Strain: Saby31

Molecule: V-Type Proton Atpase Subunit H
Chain: P
Synonym: V-Atpase Subunit H, V-Atpase 54 Kda Subunit, Vacuo Pump Subunit H;
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Strain: Saby31

Molecule: V-Type Proton Atpase Subunit C
Chain: R, U, X, Y, W, Z, V, a, S, T
Synonym: V-Atpase Subunit C, Guanine Nucleotide Exchange Fa Atpase 16 Kda Proteolipid Subunit 1, Vacuolar Proton Pump C
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Strain: Saby31
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 8.30 Å
ligand
enzyme Hydrolase E.C.3.6.3.14 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
E, C, A


F, B, D


K, I, G


L, J, H


M
  • ATPase activity, coupled to ...
  • proton-transporting ATPase a...


    • N


    O


    P


    Q


    S, a, T, Y, V, Z, W, X, R, U


    b


    Primary referenceElectron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase., Zhao J, Benlekbir S, Rubinstein JL, Nature. 2015 May 14;521(7551):241-5. doi: 10.1038/nature14365. PMID:25971514
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (975 Kb) [Save to disk]
  • Biological Unit Coordinates (3j9v.pdb1.gz) 965 Kb
  • CSU: Contacts of Structural Units for 3J9V
  • Retrieve 3J9V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J9V from S2C, [Save to disk]
    • View 3J9V in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3J9V
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3J9V, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j9v] [3j9v_U] [3j9v_Y] [3j9v_C] [3j9v_N] [3j9v_Q] [3j9v_G] [3j9v_P] [3j9v_K] [3j9v_F] [3j9v_V] [3j9v_R] [3j9v_a] [3j9v_H] [3j9v_Z] [3j9v_X] [3j9v_W] [3j9v_B] [3j9v_J] [3j9v_E] [3j9v_L] [3j9v_S] [3j9v_D] [3j9v_A] [3j9v_M] [3j9v_I] [3j9v_O] [3j9v_T] [3j9v_b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3J9V: [AAA ] by SMART
    • Other resources with information on 3J9V
  • Community annotation for 3J9V at PDBWiki (http://pdbwiki.org)

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