+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26150 | |||||||||
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Title | Cytoplasmic domain of ankyrin complex (B2P1A1) | |||||||||
Map data | Cytoplasmic domain of Ankyrin complex (B2P1A1) | |||||||||
Sample |
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Keywords | Red blood cell / Ankyrin complex / membrane protein / band 3 / protein 4.2 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Xia X / Liu SH / Zhou ZH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Structure, dynamics and assembly of the ankyrin complex on human red blood cell membrane. Authors: Xian Xia / Shiheng Liu / Z Hong Zhou / Abstract: The cytoskeleton of a red blood cell (RBC) is anchored to the cell membrane by the ankyrin complex. This complex is assembled during RBC genesis and comprises primarily band 3, protein 4.2 and ...The cytoskeleton of a red blood cell (RBC) is anchored to the cell membrane by the ankyrin complex. This complex is assembled during RBC genesis and comprises primarily band 3, protein 4.2 and ankyrin, whose mutations contribute to numerous human inherited diseases. High-resolution structures of the ankyrin complex have been long sought-after to understand its assembly and disease-causing mutations. Here, we analyzed native complexes on the human RBC membrane by stepwise fractionation. Cryo-electron microscopy structures of nine band-3-associated complexes reveal that protein 4.2 stabilizes the cytoplasmic domain of band 3 dimer. In turn, the superhelix-shaped ankyrin binds to this protein 4.2 via ankyrin repeats (ARs) 6-13 and to another band 3 dimer via ARs 17-20, bridging two band 3 dimers in the ankyrin complex. Integration of these structures with both prior data and our biochemical data supports a model of ankyrin complex assembly during erythropoiesis and identifies interactions essential for the mechanical stability of RBC. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26150.map.gz | 203.8 MB | EMDB map data format | |
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Header (meta data) | emd-26150-v30.xml emd-26150.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
Images | emd_26150.png | 76.1 KB | ||
Filedesc metadata | emd-26150.cif.gz | 4.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26150 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26150 | HTTPS FTP |
-Validation report
Summary document | emd_26150_validation.pdf.gz | 492.3 KB | Display | EMDB validaton report |
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Full document | emd_26150_full_validation.pdf.gz | 491.8 KB | Display | |
Data in XML | emd_26150_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_26150_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26150 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26150 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26150.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cytoplasmic domain of Ankyrin complex (B2P1A1) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : High-salt fraction 2 from human red blood cell membrane
Entire | Name: High-salt fraction 2 from human red blood cell membrane |
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Components |
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-Supramolecule #1: High-salt fraction 2 from human red blood cell membrane
Supramolecule | Name: High-salt fraction 2 from human red blood cell membrane type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 480 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 100.0 K / Max: 100.0 K |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 21187 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 155 |
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