+Open data
-Basic information
Entry | Database: PDB / ID: 7uzh | ||||||
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Title | Rat Kidney V-ATPase with SidK, State 2 | ||||||
Components |
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Keywords | PROTON TRANSPORT / V-ATPase / Complex / Membrane protein | ||||||
Function / homology | Function and homology information Metabolism of Angiotensinogen to Angiotensins / eye pigmentation / central nervous system maturation / Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / transporter activator activity / negative regulation of autophagic cell death / Insulin receptor recycling / RHOA GTPase cycle ...Metabolism of Angiotensinogen to Angiotensins / eye pigmentation / central nervous system maturation / Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / transporter activator activity / negative regulation of autophagic cell death / Insulin receptor recycling / RHOA GTPase cycle / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / proton-transporting V-type ATPase, V0 domain / plasma membrane proton-transporting V-type ATPase complex / extrinsic component of synaptic vesicle membrane / lysosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / intracellular organelle / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / NURF complex / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / head morphogenesis / vacuolar acidification / protein localization to cilium / transmembrane transporter complex / dendritic spine membrane / regulation of cellular pH / osteoclast development / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / ATPase activator activity / autophagosome membrane / regulation of MAPK cascade / microvillus / MLL1 complex / positive regulation of Wnt signaling pathway / cilium assembly / angiotensin maturation / regulation of macroautophagy / axon terminus / ATP metabolic process / phagocytic vesicle / H+-transporting two-sector ATPase / RNA endonuclease activity / ruffle / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / secretory granule / cilium / transmembrane transport / terminal bouton / synaptic vesicle membrane / small GTPase binding / endocytosis / positive regulation of canonical Wnt signaling pathway / melanosome / synaptic vesicle / apical part of cell / signaling receptor activity / cell body / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / early endosome / endosome membrane / endosome / apical plasma membrane / lysosomal membrane / axon / external side of plasma membrane / centrosome / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / extracellular space / nucleoplasm / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Legionella pneumophila (bacteria) Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Rubinstein, J.L. / Abbas, Y.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: Structure of V-ATPase with NCOA7B Authors: Abbas, Y.M. / Rubinstein, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uzh.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7uzh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7uzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/7uzh ftp://data.pdbj.org/pub/pdb/validation_reports/uz/7uzh | HTTPS FTP |
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-Related structure data
Related structure data | 26911MC 7uzfC 7uzgC 7uziC 7uzjC 7uzkC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-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) Rattus norvegicus (Norway rat) / References: UniProt: D4A133 #4: Protein | | Mass: 28359.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6P503 |
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-V-type proton ATPase ... , 11 types, 25 molecules DEFGIJKLMNOPacdeghijklmno
#2: Protein | Mass: 56611.570 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62815 #3: Protein | | Mass: 43958.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5FVI6 #5: Protein | Mass: 26167.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6PCU2 #6: Protein | | Mass: 13389.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P50408 #7: Protein | Mass: 13733.393 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: B2GUV5 #8: Protein | | Mass: 55936.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A0G2K9J2 #10: Protein | | Mass: 96429.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P25286 #12: Protein | | Mass: 51160.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: O54715 #13: Protein | | Mass: 40341.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5M7T6 #14: Protein | | Mass: 9203.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5EB76 #16: Protein | Mass: 15815.833 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P63081 |
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-Protein , 4 types, 6 molecules QRSbfp
#9: Protein | Mass: 34693.605 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZWW6 #11: Protein | | Mass: 21618.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: B0K022 #15: Protein | | Mass: 11000.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: D3ZIM6 #17: Protein | | Mass: 39118.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6AXS4 |
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-Non-polymers , 1 types, 1 molecules
#18: Chemical | ChemComp-ADP / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Rat Kidney V-ATPase with SidK / Type: COMPLEX / Entity ID: #1-#17 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3800 nm / Nominal defocus min: 100 nm |
Image recording | Electron dose: 44.825 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.8 Å / Resolution method: OTHER / Num. of particles: 46604 Details: Model-map FSC (threshold 0.5) calculated in phenix.validation_cryoem Symmetry type: POINT |