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TitleV1EG of V/A-ATPase from Thermus thermophilus high ATP state1-2
AuthorsKishikawa J, Nakanishi A, Nakano A, Saeki S, Furuta A, Kato T, Mitsuoka K, Yokoyama K
MethodSingle Particle(Reported Resolution 3.2 Å)PDB:7vam
EMDB image
Primary CitationStructural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases. Kishikawa J, Nakanishi A, Nakano A, Saeki S, Furuta A, Kato T, Mistuoka K, Yokoyama K Nat Commun (2022) PubMed DOI show all entries for this citation
Funding SourceMinistry of Education, Culture, Sports, Science and Technology (Japan), Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)
StatusDepositedReleasedLast Update
REL2021-08-302022-07-132024-06-19

Name: V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state1-2SpecimenType: particle MW: 0.4 MDa pH: 8

Component Typescomplex
Component Names

V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state1-2

Molecular Typesligand, protein
Molecule Names
  • ADENOSINE-5'-DIPHOSPHATE
  • ADENOSINE-5'-TRIPHOSPHATE
  • MAGNESIUM ION
  • PHOSPHATE ION
  • V-type ATP synthase alpha chain
  • V-type ATP synthase beta chain
  • V-type ATP synthase subunit D
  • V-type ATP synthase subunit E
  • V-type ATP synthase subunit F
  • V-type ATP synthase, subunit G
Sources

Thermus thermophilus HB8 ncbi:300852

Ligand IDs: ADP MG PO4 ATP

Fitting Details: The atomic model built in this study was used as an initial model.

Specimen Preparationvitrification
VitrificationFEI VITROBOT MARK IV
MicroscopeFEI TITAN KRIOS (300 kV)
Specimen HolderFEI TITAN KRIOS AUTOGRID HOLDER
DetectorGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose50 (e/sq. Å)
Number of Particles28801
Imposed SymmetryC1
Reconstruction SoftwareRELION
Fitting ProtocolOTHER

Details: V1EG of V/A-ATPase from Thermus thermophilus, state1-2

Map File Size108 Mbytes
Voxel Dimensions (Å)0.88 x 0.88 x 0.88
Map Dimensions (voxels) 300 x 300 x 300
Map Data Type IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Density StatisticsMin -0.062Max 0.125Avg 0Std 0.006
Recommended Contour Level0.022 (3.6 σ)
Mol*3DViewer Map Visual Analysis @ EMDB
Header Metadataemd-31850.xml emd-31850.cif.gz
Primary Mapemd_31850.map.gz (108 Mbytes)
Masksemd_31850_msk_1.map
Imagesemd_31850.png
FSC Curvesemd_31850_fsc.xml
Half Maps
V1EG of V/A-ATPase from Thermus thermophilus, state1-2, half map Aemd_31850_half_map_2.map.gz
V1EG of V/A-ATPase from Thermus thermophilus, state1-2, half map Aemd_31850_half_map_1.map.gz
Fitted PDB7vam


Current: files.wwpdb.org (USA)

wwPDB Map Validation Reportemd_31850_full_validation.pdf.gz
wwPDB Model Validation Report7vam_full_validation.pdf.gz
View EMDB map entry EMD-31850: EMDB PDBj 3Dbionotes
View associated model PDB 7vam: RCSB-PDB PDBe PDBj