+Open data
-Basic information
Entry | Database: PDB / ID: 8csl | ||||||
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Title | Sub-tomogram averaging of erythrocyte ankyrin-1 complex | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/STRUCTURAL PROTEIN / Membrane protein / ankyrin complex / TRANSPORT PROTEIN-STRUCTURAL PROTEIN complex | ||||||
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) | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 25 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 | 8csl.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8csl.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8csl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8csl_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8csl_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8csl_validation.xml.gz | 133.9 KB | Display | |
Data in CIF | 8csl_validation.cif.gz | 240.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/8csl ftp://data.pdbj.org/pub/pdb/validation_reports/cs/8csl | HTTPS FTP |
-Related structure data
Related structure data | 26965MC 7uz3C 7uzeC 7uzqC 7uzsC 7uzuC 7uzvC 7v07C 7v0kC 7v0mC 7v0qC 7v0sC 7v0tC 7v0uC 7v0xC 7v0yC 7v19C 8crqC 8crrC 8crtC 8cs9C 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
-Protein , 7 types, 19 molecules AWVeYfZgKLQXPRaSbTc
#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.: 7 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02730 #3: Protein | | Mass: 45598.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18577 #4: Protein | Mass: 44229.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02094 #5: Protein | | Mass: 77096.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P16452 #6: Protein | | Mass: 9789.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P06028 #7: Protein | Mass: 16348.433 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02724 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Sub-tomogram average of ankyrin-1 complexes from native erythrocyte vesicles Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 / Details: 130 mM KCl, 10 mM HEPES, pH 7.4 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Ghost membranes (~100 mg) were pelleted (6,000 x g, 10 minutes), washed 5 times in 130 mM KCl, 10 mM HEPES, pH 7.4, and then homogenized with the same buffer. The sample was sonicated using ...Details: Ghost membranes (~100 mg) were pelleted (6,000 x g, 10 minutes), washed 5 times in 130 mM KCl, 10 mM HEPES, pH 7.4, and then homogenized with the same buffer. The sample was sonicated using microprobe (amplitude = 30, pulse on = 5 sec, rest time = 10 sec, total pulse on = 50 sec). Large fragments are removed by centrifugation (6,000 x g, 10 minutes) and the supernatant was extruded (Avanti Polar Lipid) 10 times using a 400 nm filter. After extrusion, vesicles were collected by ultra-centrifugation at 35,000 rpm for 30 minutes (S120-AT3, Sorvall). The pellet, which contains vesicles, was resuspended at a final concentration of 5 mg/mL. All steps were performed at room temperature to facilitate vesicle formation. |
Vitrification | Cryogen name: ETHANE |
-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: 5000 nm / Nominal defocus min: 3000 nm / Cs: 0.01 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 3.14 e/Å2 / Avg electron dose per subtomogram: 113 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Details: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||
3D reconstruction | Resolution: 25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1596 / Symmetry type: POINT | |||||||||
EM volume selection | Details: Picked using crYOLO, trained using manual picks. / Num. of tomograms: 100 / Num. of volumes extracted: 60029 | |||||||||
Atomic model building | Protocol: RIGID BODY FIT Details: Erythrocyte ankyrin-1 complex (Class1, 8CS9) was rigid fit as a single body to the map using fitmap in UCSF Chimera, after which waters, ligands and sidechains were removed from the model. | |||||||||
Atomic model building | PDB-ID: 8CS9 Accession code: 8CS9 / Source name: PDB / Type: experimental model |