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Yorodumi- PDB-7uze: Erythrocyte ankyrin-1 complex class 2 local refinement of AQP1 (C... -
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-Basic information
Entry | Database: PDB / ID: 7uze | ||||||
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Title | Erythrocyte ankyrin-1 complex class 2 local refinement of AQP1 (C4 symmetry applied) | ||||||
Components | Aquaporin-1 | ||||||
Keywords | TRANSPORT PROTEIN / Membrane Protein / Anion Exchange / Erythrocyte / Glycoprotein | ||||||
Function / homology | Function and homology information nitric oxide transmembrane transporter activity / metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / cerebrospinal fluid secretion / lipid digestion / cellular response to salt stress / renal water transport / glycerol transmembrane transporter activity ...nitric oxide transmembrane transporter activity / metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / cerebrospinal fluid secretion / lipid digestion / cellular response to salt stress / renal water transport / glycerol transmembrane transporter activity / corticotropin secretion / secretory granule organization / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / renal water absorption / positive regulation of saliva secretion / Passive transport by Aquaporins / glycerol transmembrane transport / water transmembrane transporter activity / establishment or maintenance of actin cytoskeleton polarity / pancreatic juice secretion / cellular response to mercury ion / lateral ventricle development / potassium ion transmembrane transporter activity / : / intracellular water homeostasis / water transport / water channel activity / transepithelial water transport / glomerular filtration / ammonium transmembrane transport / ankyrin-1 complex / intracellularly cGMP-activated cation channel activity / ammonium channel activity / camera-type eye morphogenesis / fibroblast migration / multicellular organismal-level water homeostasis / cellular homeostasis / hyperosmotic response / cellular hyperosmotic response / renal water homeostasis / cell volume homeostasis / positive regulation of fibroblast migration / odontogenesis / cellular response to nitric oxide / nitric oxide transport / cGMP-mediated signaling / brush border / transmembrane transporter activity / potassium channel activity / cellular response to dexamethasone stimulus / basal plasma membrane / cellular response to retinoic acid / cellular response to cAMP / sensory perception of pain / cellular response to copper ion / ephrin receptor binding / potassium ion transport / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / establishment of localization in cell / brush border membrane / wound healing / carbon dioxide transport / cellular response to mechanical stimulus / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / sarcolemma / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of fibroblast proliferation / cellular response to hydrogen peroxide / positive regulation of angiogenesis / cellular response to UV / apical part of cell / cellular response to hypoxia / basolateral plasma membrane / nuclear membrane / defense response to Gram-negative bacterium / apical plasma membrane / axon / negative regulation of apoptotic process / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||
Authors | Vallese, F. / Kim, K. / Yen, L.Y. / Johnston, J.D. / Noble, A.J. / Cali, T. / Clarke, O.B. | ||||||
Funding support | 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Architecture of the human erythrocyte ankyrin-1 complex. Authors: Francesca Vallese / Kookjoo Kim / Laura Y Yen / Jake D Johnston / Alex J Noble / Tito Calì / Oliver Biggs Clarke / Abstract: The stability and shape of the erythrocyte membrane is provided by the ankyrin-1 complex, but how it tethers the spectrin-actin cytoskeleton to the lipid bilayer and the nature of its association ...The stability and shape of the erythrocyte membrane is provided by the ankyrin-1 complex, but how it tethers the spectrin-actin cytoskeleton to the lipid bilayer and the nature of its association with the band 3 anion exchanger and the Rhesus glycoproteins remains unknown. Here we present structures of ankyrin-1 complexes purified from human erythrocytes. We reveal the architecture of a core complex of ankyrin-1, the Rhesus proteins RhAG and RhCE, the band 3 anion exchanger, protein 4.2, glycophorin A and glycophorin B. The distinct T-shaped conformation of membrane-bound ankyrin-1 facilitates recognition of RhCE and, unexpectedly, the water channel aquaporin-1. Together, our results uncover the molecular details of ankyrin-1 association with the erythrocyte membrane, and illustrate the mechanism of ankyrin-mediated membrane protein clustering. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uze.cif.gz | 350.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uze.ent.gz | 299.8 KB | Display | PDB format |
PDBx/mmJSON format | 7uze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uze_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7uze_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7uze_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 7uze_validation.cif.gz | 64.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/7uze ftp://data.pdbj.org/pub/pdb/validation_reports/uz/7uze | HTTPS FTP |
-Related structure data
Related structure data | 26886MC 7uz3C 7uzqC 7uzsC 7uzuC 7uzvC 7v07C 7v0kC 7v0mC 7v0qC 7v0sC 7v0tC 7v0uC 7v0xC 7v0yC 7v19C 8crqC 8crrC 8crtC 8cs9C 8cslC 8csvC 8cswC 8csxC 8csyC 8ct2C 8ct3C 8cteC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.6019/EMPIAR-11043 / Data set type: EMPIAR |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 28788.320 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Palmitoylated at Cys-87 / Source: (natural) Homo sapiens (human) / Organ: Blood / Tissue: Erythrocytes / References: UniProt: P29972 #2: Chemical | ChemComp-CLR / #3: Water | ChemComp-HOH / | 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: Local refinement of aquaporin 1 in class 2 of ankyrin complex; local C4 symmetry applied. Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) / Cellular location: Plasma membrane / Organ: Blood / Tissue: Erythrocytes |
Buffer solution | pH: 7.4 Details: Final gel filtration buffer contained 0.05 % (w/v) digitonin, 130mM KCl, 20mM HEPES pH 7.4, 1mM ATP, 1mM MgCl2, 1mM PMSF. Peak fractions were concentrated to 8mg/mL, and 0.01% (w/v) of ...Details: Final gel filtration buffer contained 0.05 % (w/v) digitonin, 130mM KCl, 20mM HEPES pH 7.4, 1mM ATP, 1mM MgCl2, 1mM PMSF. Peak fractions were concentrated to 8mg/mL, and 0.01% (w/v) of glycyrrhizic acid was added immediately prior to vitrification. |
Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Ankyrin complex mixture, purified from digitonin-solubilized erythrocyte ghost membranes. |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 4-6 seconds, wait time 30 seconds. |
-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 FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.5 sec. / Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 14464 / Details: Two grids were imaged in a single session. |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Details: Patch CTF (cryoSPARC v3) followed by per particle defocus refinement and refinement of higher order aberrations (cryoSPARC v3) Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108425 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4CSK Pdb chain-ID: A | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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