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- EMDB-26912: Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Rat Kidney V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 | |||||||||
![]() | V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 | |||||||||
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![]() | V-ATPase / Complex / Membrane protein / PROTON TRANSPORT | |||||||||
Function / homology | ![]() Metabolism of Angiotensinogen to Angiotensins / Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / RHOA GTPase cycle / Insulin receptor recycling / eye pigmentation / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death ...Metabolism of Angiotensinogen to Angiotensins / Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / RHOA GTPase cycle / Insulin receptor recycling / eye pigmentation / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / 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 / intracellular organelle / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / plasma membrane proton-transporting V-type ATPase complex / lysosomal lumen acidification / NURF complex / clathrin-coated vesicle membrane / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / proton-transporting V-type ATPase complex / head morphogenesis / protein localization to cilium / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / osteoclast development / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / autophagosome membrane / microvillus / regulation of MAPK cascade / ATPase activator activity / MLL1 complex / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / regulation of macroautophagy / angiotensin maturation / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / ruffle / RNA endonuclease activity / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / secretory granule / terminal bouton / transmembrane transport / synaptic vesicle membrane / small GTPase binding / cilium / melanosome / positive regulation of canonical Wnt signaling pathway / 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 / positive regulation of ERK1 and ERK2 cascade / lysosome / early endosome / endosome membrane / endosome / apical plasma membrane / lysosomal membrane / external side of plasma membrane / axon / 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 / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Rubinstein JL / Abbas YM | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of V-ATPase with NCOA7B Authors: Abbas YM / Rubinstein JL | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 23.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.3 KB 28.3 KB | Display Display | ![]() |
Images | ![]() | 76.2 KB | ||
Filedesc metadata | ![]() | 9.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 365.4 KB | Display | ![]() |
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Full document | ![]() | 364.9 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uziMC ![]() 7uzfC ![]() 7uzgC ![]() 7uzhC ![]() 7uzjC ![]() 7uzkC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | V-ATPase lacking subunit H, with SidK and NCOA7B, State 2 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.3225 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Rat Kidney V-ATPase with SidK
+Supramolecule #1: Rat Kidney V-ATPase with SidK
+Macromolecule #1: ATPase H+-transporting V1 subunit A
+Macromolecule #2: V-type proton ATPase subunit B, brain isoform
+Macromolecule #3: V-type proton ATPase subunit C 1
+Macromolecule #4: ATPase H+-transporting V1 subunit D
+Macromolecule #5: V-type proton ATPase subunit E 1
+Macromolecule #6: V-type proton ATPase subunit F
+Macromolecule #7: V-type proton ATPase subunit G
+Macromolecule #8: V-type proton ATPase subunit H
+Macromolecule #9: Nuclear receptor coactivator 7
+Macromolecule #10: V-type proton ATPase 116 kDa subunit a isoform 1
+Macromolecule #11: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
+Macromolecule #12: V-type proton ATPase subunit S1
+Macromolecule #13: V-type proton ATPase subunit
+Macromolecule #14: V-type proton ATPase subunit e 2
+Macromolecule #15: Ribonuclease K
+Macromolecule #16: V-type proton ATPase 16 kDa proteolipid subunit
+Macromolecule #17: Renin receptor
+Macromolecule #18: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 44.825 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 0.1 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: OTHER Details: Model-map FSC (threshold 0.5) calculated in phenix.validation_cryoem Number images used: 32453 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |