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Yorodumi- PDB-8csv: Local refinement of Anykyrin-1 (N-terminal half of membrane bindi... -
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-Basic information
Entry | Database: PDB / ID: 8csv | ||||||
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Title | Local refinement of Anykyrin-1 (N-terminal half of membrane binding domain) in Class 2 of erythrocyte ankyrin-1 complex | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/STRUCTURAL PROTEIN / Membrane Protein / Anion Exchange / Erythrocyte / Glycoprotein / TRANSPORT PROTEIN-STRUCTURAL PROTEIN complex | ||||||
Function / homology | Function and homology information spectrin-associated cytoskeleton / positive regulation of organelle organization / maintenance of epithelial cell apical/basal polarity / pH elevation / Defective SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA) / negative regulation of urine volume / NrCAM interactions / Neurofascin interactions / Bicarbonate transporters / intracellular monoatomic ion homeostasis ...spectrin-associated cytoskeleton / positive regulation of organelle organization / maintenance of epithelial cell apical/basal polarity / pH elevation / Defective SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA) / negative regulation of urine volume / NrCAM interactions / Neurofascin interactions / Bicarbonate transporters / intracellular monoatomic ion homeostasis / ankyrin-1 complex / CHL1 interactions / plasma membrane phospholipid scrambling / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / cytoskeletal anchor activity / solute:inorganic anion antiporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / M band / monoatomic anion transport / Interaction between L1 and Ankyrins / chloride transport / chloride transmembrane transporter activity / ankyrin binding / negative regulation of glycolytic process through fructose-6-phosphate / spectrin binding / hemoglobin binding / cortical cytoskeleton / exocytosis / axolemma / endoplasmic reticulum to Golgi vesicle-mediated transport / erythrocyte development / COPI-mediated anterograde transport / protein-membrane adaptor activity / chloride transmembrane transport / cytoskeleton organization / sarcoplasmic reticulum / protein localization to plasma membrane / regulation of intracellular pH / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / sarcolemma / transmembrane transport / Z disc / blood coagulation / ATPase binding / basolateral plasma membrane / protein phosphatase binding / postsynaptic membrane / transmembrane transporter binding / blood microparticle / cytoskeleton / neuron projection / enzyme binding / structural molecule activity / signal transduction / protein homodimerization activity / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 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 | 8csv.cif.gz | 152.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8csv.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 8csv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8csv_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8csv_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8csv_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 8csv_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/8csv ftp://data.pdbj.org/pub/pdb/validation_reports/cs/8csv | HTTPS FTP |
-Related structure data
Related structure data | 26972MC 7uz3C 7uzeC 7uzqC 7uzsC 7uzuC 7uzvC 7v07C 7v0kC 7v0mC 7v0qC 7v0sC 7v0tC 7v0uC 7v0xC 7v0yC 7v19C 8crqC 8crrC 8crtC 8cs9C 8cslC 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: 206522.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P16157 |
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#2: Protein | Mass: 101883.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02730 |
#3: Water | ChemComp-HOH / |
-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: Class 2 of the erythrocyte ankyrin-1 complex (local refinement of N-terminal half of membrane binding domain, bound to N-terminal peptide of band3) Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 Details: Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v ...Details: Final gel filtration buffer contained 0.05% w/v digitonin, 130 mM KCl, 20 mM HEPES, pH 7.4, 1 mM ATP, 1 mM MgCl2, 1 mM PMSF. Peak fractions were concentrated to 8 mg/mL, and 0.01% w/v 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: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145645 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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