[English] 日本語
![](img/lk-miru.gif)
- PDB-6vq6: Mammalian V-ATPase from rat brain - composite model of rotational... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6vq6 | ||||||
---|---|---|---|---|---|---|---|
Title | Mammalian V-ATPase from rat brain - composite model of rotational state 1 bound to ADP and SidK (built from focused refinement models) | ||||||
![]() |
| ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() Metabolism of Angiotensinogen to Angiotensins / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Abbas, Y.M. / Rubinstein, J.L. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure of V-ATPase from the mammalian brain. Authors: Yazan M Abbas / Di Wu / Stephanie A Bueler / Carol V Robinson / John L Rubinstein / ![]() ![]() Abstract: In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes ...In neurons, the loading of neurotransmitters into synaptic vesicles uses energy from proton-pumping vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases). These membrane protein complexes possess numerous subunit isoforms, which complicates their analysis. We isolated homogeneous rat brain V-ATPase through its interaction with SidK, a effector protein. Cryo-electron microscopy allowed the construction of an atomic model, defining the enzyme's ATP:proton ratio as 3:10 and revealing a homolog of yeast subunit f in the membrane region, which we tentatively identify as RNAseK. The c ring encloses the transmembrane anchors for cleaved ATP6AP1/Ac45 and ATP6AP2/PRR, the latter of which is the (pro)renin receptor that, in other contexts, is involved in both Wnt signaling and the renin-angiotensin system that regulates blood pressure. This structure shows how ATP6AP1/Ac45 and ATP6AP2/PRR enable assembly of the enzyme's catalytic and membrane regions. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 21317MC ![]() 6vq7C ![]() 6vq8C ![]() 6vq9C ![]() 6vqaC ![]() 6vqbC ![]() 6vqcC ![]() 6vqgC ![]() 6vqhC ![]() 6vqiC ![]() 6vqjC ![]() 6vqkC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-ATPase H+-transporting V1 subunit ... , 2 types, 4 molecules ABCH
#1: Protein | Mass: 68341.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #4: Protein | | Mass: 28359.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
---|
-V-type proton ATPase ... , 10 types, 24 molecules DEFGIJKLMNOacdeghijklmno
#2: Protein | Mass: 56611.570 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #3: Protein | | Mass: 43958.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #5: Protein | Mass: 26167.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #6: Protein | | Mass: 13389.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #7: Protein | Mass: 13690.476 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #9: Protein | | Mass: 96429.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #11: Protein | | Mass: 51160.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #12: Protein | | Mass: 40341.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #13: Protein | | Mass: 9203.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #15: Protein | Mass: 15815.833 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
---|
-Protein , 4 types, 6 molecules QRSbfp
#8: Protein | Mass: 34693.605 Da / Num. of mol.: 3 / Fragment: N-terminal fragment with 3x FLAG tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0968 / Production host: ![]() ![]() ![]() #10: Protein | | ![]() Mass: 21618.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #14: Protein | | Mass: 11000.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #16: Protein | | ![]() Mass: 39118.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
---|
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#17: Chemical | ChemComp-ADP / ![]() |
---|---|
#18: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
-
Sample preparation
Component | Name: Rat brain V-ATPase complex bound to the Legionella pneumophila effector protein SidK Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE-PROPANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 43 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-
Processing
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
Symmetry | Point symmetry![]() |
3D reconstruction![]() | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90648 / Algorithm: BACK PROJECTION / Symmetry type: POINT |
Atomic model building | Details: Final composite model was built from focused refinement models that were built into their corresponding focused refinement maps and subsequently aligned against the overall map before ...Details: Final composite model was built from focused refinement models that were built into their corresponding focused refinement maps and subsequently aligned against the overall map before combining into the composite model. The composite model was not refined against the data. |