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Yorodumi- EMDB-26960: Composite reconstruction of Class 1 of the erythrocyte ankyrin-1 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26960 | |||||||||
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Title | Composite reconstruction of Class 1 of the erythrocyte ankyrin-1 complex | |||||||||
Map data | Composite reconstruction of EMDs: 26944, 26948, 26949, 26950, 26951, 26952, 26953, 26955, 26954, 26956, 26958 aligned to the consensus refinement. | |||||||||
Sample |
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Function / homology | Function and homology information methylammonium transmembrane transport / Defective RHAG causes regulator type Rh-null hemolytic anemia (RHN) / Rhesus blood group biosynthesis / methylammonium transmembrane transporter activity / Rhesus glycoproteins mediate ammonium transport / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / ammonium homeostasis / spectrin-associated cytoskeleton / hemoglobin metabolic process ...methylammonium transmembrane transport / Defective RHAG causes regulator type Rh-null hemolytic anemia (RHN) / Rhesus blood group biosynthesis / methylammonium transmembrane transporter activity / Rhesus glycoproteins mediate ammonium transport / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / ammonium homeostasis / spectrin-associated cytoskeleton / hemoglobin metabolic process / positive regulation of organelle organization / protein-glutamine gamma-glutamyltransferase activity / leak channel activity / 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 / ammonium transmembrane transport / Neurofascin interactions / Bicarbonate transporters / intracellular monoatomic ion homeostasis / ankyrin-1 complex / ammonium channel activity / 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 / monoatomic anion transport / bicarbonate transmembrane transporter activity / M band / inorganic cation transmembrane transport / Interaction between L1 and Ankyrins / chloride transport / chloride transmembrane transporter activity / ankyrin binding / negative regulation of glycolytic process through fructose-6-phosphate / hemoglobin binding / spectrin binding / cortical cytoskeleton / erythrocyte maturation / exocytosis / axolemma / endoplasmic reticulum to Golgi vesicle-mediated transport / erythrocyte development / COPI-mediated anterograde transport / protein-membrane adaptor activity / spleen development / chloride transmembrane transport / cytoskeleton organization / sarcoplasmic reticulum / protein localization to plasma membrane / regulation of intracellular pH / Cell surface interactions at the vascular wall / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / cell morphogenesis / Erythrocytes take up carbon dioxide and release oxygen / sarcolemma / structural constituent of cytoskeleton / transmembrane transport / cytoplasmic side of plasma membrane / Z disc / multicellular organismal-level iron ion homeostasis / blood coagulation / virus receptor activity / regulation of cell shape / ATPase binding / basolateral plasma membrane / protein phosphatase binding / postsynaptic membrane / transmembrane transporter binding / blood microparticle / cytoskeleton / neuron projection / structural molecule activity / enzyme binding / signal transduction / protein homodimerization activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.74 Å | |||||||||
Authors | Vallese F / Kim K / Yen LY / Johnston JD / Noble AJ / Cali T / Clarke OB | |||||||||
Funding support | 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26960.map.gz | 57.3 MB | EMDB map data format | |
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Header (meta data) | emd-26960-v30.xml emd-26960.xml | 45.1 KB 45.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26960_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_26960.png | 119.5 KB | ||
Others | emd_26960_additional_1.map.gz emd_26960_additional_2.map.gz emd_26960_additional_3.map.gz emd_26960_additional_4.map.gz emd_26960_additional_5.map.gz emd_26960_additional_6.map.gz emd_26960_additional_7.map.gz emd_26960_additional_8.map.gz | 328.1 MB 322.9 MB 173.3 MB 71.3 MB 322.9 MB 324.4 MB 444.7 MB 1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26960 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26960 | HTTPS FTP |
-Validation report
Summary document | emd_26960_validation.pdf.gz | 400.1 KB | Display | EMDB validaton report |
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Full document | emd_26960_full_validation.pdf.gz | 399.6 KB | Display | |
Data in XML | emd_26960_validation.xml.gz | 15 KB | Display | |
Data in CIF | emd_26960_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26960 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26960 | HTTPS FTP |
-Related structure data
Related structure data | 8cs9MC 7uz3C 7uzeC 7uzqC 7uzsC 7uzuC 7uzvC 7v07C 7v0kC 7v0mC 7v0qC 7v0sC 7v0tC 7v0uC 7v0xC 7v0yC 7v19C 8crqC 8crrC 8crtC 8cslC 8csvC 8cswC 8csxC 8csyC 8ct2C 8ct3C 8cteC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26960.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite reconstruction of EMDs: 26944, 26948, 26949, 26950, 26951, 26952, 26953, 26955, 26954, 26956, 26958 aligned to the consensus refinement. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Consensus refinement (sharpened).
File | emd_26960_additional_1.map | ||||||||||||
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Annotation | Consensus refinement (sharpened). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Consensus refinement (half map 1)
File | emd_26960_additional_2.map | ||||||||||||
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Annotation | Consensus refinement (half map 1) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Consensus refinement (unsharpened).
File | emd_26960_additional_3.map | ||||||||||||
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Annotation | Consensus refinement (unsharpened). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Composite reconstruction of EMDs: 26944, 26948, 26949, 26950,...
File | emd_26960_additional_4.map | ||||||||||||
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Annotation | Composite reconstruction of EMDs: 26944, 26948, 26949, 26950, 26951, 26952, 26953, 26955, 26954, 26956, 26958 aligned to the consensus refinement. Unsharpened. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Consensus refinement (half map 1)
File | emd_26960_additional_5.map | ||||||||||||
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Annotation | Consensus refinement (half map 1) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Composite reconstruction of EMDs: 26944, 26948, 26949, 26950,...
File | emd_26960_additional_6.map | ||||||||||||
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Annotation | Composite reconstruction of EMDs: 26944, 26948, 26949, 26950, 26951, 26952, 26953, 26955, 26954, 26956, 26958 aligned to the consensus refinement. Unsharpened, filtered to 4A to aid visualization. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Composite reconstruction of EMDs: 26944, 26948, 26949, 26950,...
File | emd_26960_additional_7.map | ||||||||||||
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Annotation | Composite reconstruction of EMDs: 26944, 26948, 26949, 26950, 26951, 26952, 26953, 26955, 26954, 26956, 26958 aligned to the consensus refinement. Resampled on 2x finer grid to aid visualization. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Mask used for FSC calculation of consensus refinement
File | emd_26960_additional_8.map | ||||||||||||
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Annotation | Mask used for FSC calculation of consensus refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Class 1 of erythrocyte ankyrin complex (composite map)
+Supramolecule #1: Class 1 of erythrocyte ankyrin complex (composite map)
+Macromolecule #1: Ankyrin-1
+Macromolecule #2: Blood group Rh(CE) polypeptide
+Macromolecule #3: Ammonium transporter Rh type A
+Macromolecule #4: Protein 4.2
+Macromolecule #5: Glycophorin-B
+Macromolecule #6: Glycophorin-A
+Macromolecule #7: Band 3 anion transport protein
+Macromolecule #9: CHOLESTEROL
+Macromolecule #10: Digitonin
+Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #12: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...
+Macromolecule #13: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8 mg/mL |
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Buffer | 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. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 4-6 seconds, wait time 30 seconds. |
Details | Ankyrin complex mixture purified from digitonin-solubilized erythrocyte ghost membranes |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 14464 / Average exposure time: 2.5 sec. / Average electron dose: 58.0 e/Å2 / Details: Two grids were imaged in a single session. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |