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Yorodumi- EMDB-26952: Local refinement of ankyrin-1 (C-terminal half), class 1 of eryth... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26952 | |||||||||
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Title | Local refinement of ankyrin-1 (C-terminal half), class 1 of erythrocyte ankyrin-1 complex | |||||||||
Map data | Main map used for model building/refinement. Density modified and cropped with phenix.resolve_cryo_em, and resampled on fine grid with relion_image_handler. | |||||||||
Sample |
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Keywords | Membrane Protein / ankyrin complex / Erythrocyte / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information spectrin-associated cytoskeleton / positive regulation of organelle organization / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / Neurofascin interactions / ankyrin-1 complex / CHL1 interactions / cytoskeletal anchor activity / M band / Interaction between L1 and Ankyrins ...spectrin-associated cytoskeleton / positive regulation of organelle organization / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / Neurofascin interactions / ankyrin-1 complex / CHL1 interactions / cytoskeletal anchor activity / M band / Interaction between L1 and Ankyrins / spectrin binding / exocytosis / axolemma / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / cytoskeleton organization / sarcoplasmic reticulum / protein localization to plasma membrane / sarcolemma / Z disc / structural constituent of cytoskeleton / cytoplasmic side of plasma membrane / ATPase binding / basolateral plasma membrane / protein phosphatase binding / postsynaptic membrane / transmembrane transporter binding / cytoskeleton / neuron projection / structural molecule activity / enzyme binding / signal transduction / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 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_26952.map.gz | 63.9 MB | EMDB map data format | |
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Header (meta data) | emd-26952-v30.xml emd-26952.xml | 32.7 KB 32.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26952_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_26952.png | 41.4 KB | ||
Filedesc metadata | emd-26952.cif.gz | 7.2 KB | ||
Others | emd_26952_additional_1.map.gz emd_26952_additional_2.map.gz emd_26952_additional_3.map.gz emd_26952_additional_4.map.gz emd_26952_half_map_1.map.gz emd_26952_half_map_2.map.gz | 322.3 MB 322.3 MB 510.1 KB 328.2 MB 63.6 MB 63.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26952 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26952 | HTTPS FTP |
-Validation report
Summary document | emd_26952_validation.pdf.gz | 824.5 KB | Display | EMDB validaton report |
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Full document | emd_26952_full_validation.pdf.gz | 824 KB | Display | |
Data in XML | emd_26952_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | emd_26952_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26952 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26952 | HTTPS FTP |
-Related structure data
Related structure data | 7v0xMC 7uz3C 7uzeC 7uzqC 7uzsC 7uzuC 7uzvC 7v07C 7v0kC 7v0mC 7v0qC 7v0sC 7v0tC 7v0uC 7v0yC 7v19C 8crqC 8crrC 8crtC 8cs9C 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_26952.map.gz / Format: CCP4 / Size: 68.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Main map used for model building/refinement. Density modified and cropped with phenix.resolve_cryo_em, and resampled on fine grid with relion_image_handler. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.415 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Half map 1 (unmodified)
File | emd_26952_additional_1.map | ||||||||||||
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Annotation | Half map 1 (unmodified) | ||||||||||||
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Density Histograms |
-Additional map: Half map 2 (unmodified)
File | emd_26952_additional_2.map | ||||||||||||
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Annotation | Half map 2 (unmodified) | ||||||||||||
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Density Histograms |
-Additional map: Mask used for FSC calculation
File | emd_26952_additional_3.map | ||||||||||||
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Annotation | Mask used for FSC calculation | ||||||||||||
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Density Histograms |
-Additional map: B-factor sharpened map.
File | emd_26952_additional_4.map | ||||||||||||
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Annotation | B-factor sharpened map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 (cropped and resampled to match main map).
File | emd_26952_half_map_1.map | ||||||||||||
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Annotation | Half map 1 (cropped and resampled to match main map). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 (cropped and resampled to match main map).
File | emd_26952_half_map_2.map | ||||||||||||
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Annotation | Half map 2 (cropped and resampled to match main map). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Erythrocyte ankyrin-1 complex
Entire | Name: Erythrocyte ankyrin-1 complex |
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Components |
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-Supramolecule #1: Erythrocyte ankyrin-1 complex
Supramolecule | Name: Erythrocyte ankyrin-1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Purified by density gradient centrifugation and size exclusion chromatography from digitonin-solubilized erythrocyte membranes. |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Blood / Tissue: Erythrocytes / Location in cell: Plasma membrane |
-Macromolecule #1: Ankyrin-1
Macromolecule | Name: Ankyrin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 206.522625 KDa |
Sequence | String: MPYSVGFREA DAATSFLRAA RSGNLDKALD HLRNGVDINT CNQNGLNGLH LASKEGHVKM VVELLHKEII LETTTKKGNT ALHIAALAG QDEVVRELVN YGANVNAQSQ KGFTPLYMAA QENHLEVVKF LLENGANQNV ATEDGFTPLA VALQQGHENV V AHLINYGT ...String: MPYSVGFREA DAATSFLRAA RSGNLDKALD HLRNGVDINT CNQNGLNGLH LASKEGHVKM VVELLHKEII LETTTKKGNT ALHIAALAG QDEVVRELVN YGANVNAQSQ KGFTPLYMAA QENHLEVVKF LLENGANQNV ATEDGFTPLA VALQQGHENV V AHLINYGT KGKVRLPALH IAARNDDTRT AAVLLQNDPN PDVLSKTGFT PLHIAAHYEN LNVAQLLLNR GASVNFTPQN GI TPLHIAS RRGNVIMVRL LLDRGAQIET KTKDELTPLH CAARNGHVRI SEILLDHGAP IQAKTKNGLS PIHMAAQGDH LDC VRLLLQ YDAEIDDITL DHLTPLHVAA HCGHHRVAKV LLDKGAKPNS RALNGFTPLH IACKKNHVRV MELLLKTGAS IDAV TESGL TPLHVASFMG HLPIVKNLLQ RGASPNVSNV KVETPLHMAA RAGHTEVAKY LLQNKAKVNA KAKDDQTPLH CAARI GHTN MVKLLLENNA NPNLATTAGH TPLHIAAREG HVETVLALLE KEASQACMTK KGFTPLHVAA KYGKVRVAEL LLERDA HPN AAGKNGLTPL HVAVHHNNLD IVKLLLPRGG SPHSPAWNGY TPLHIAAKQN QVEVARSLLQ YGGSANAESV QGVTPLH LA AQEGHAEMVA LLLSKQANGN LGNKSGLTPL HLVAQEGHVP VADVLIKHGV MVDATTRMGY TPLHVASHYG NIKLVKFL L QHQADVNAKT KLGYSPLHQA AQQGHTDIVT LLLKNGASPN EVSSDGTTPL AIAKRLGYIS VTDVLKVVTD ETSFVLVSD KHRMSFPETV DEILDVSEDE GEELISFKAE RRDSRDVDEE KELLDFVPKL DQVVESPAIP RIPCAMPETV VIRSEEQEQA SKEYDEDSL IPSSPATETS DNISPVASPV HTGFLVSFMV DARGGSMRGS RHNGLRVVIP PRTCAAPTRI TCRLVKPQKL S TPPPLAEE EGLASRIIAL GPTGAQFLSP VIVEIPHFAS HGRGDRELVV LRSENGSVWK EHRSRYGESY LDQILNGMDE EL GSLEELE KKRVCRIITT DFPLYFVIMS RLCQDYDTIG PEGGSLKSKL VPLVQATFPE NAVTKRVKLA LQAQPVPDEL VTK LLGNQA TFSPIVTVEP RRRKFHRPIG LRIPLPPSWT DNPRDSGEGD TTSLRLLCSV IGGTDQAQWE DITGTTKLVY ANEC ANFTT NVSARFWLSD CPRTAEAVNF ATLLYKELTA VPYMAKFVIF AKMNDPREGR LRCYCMTDDK VDKTLEQHEN FVEVA RSRD IEVLEGMSLF AELSGNLVPV KKAAQQRSFH FQSFRENRLA MPVKVRDSSR EPGGSLSFLR KAMKYEDTQH ILCHLN ITM PPCAKGSGAE DRRRTPTPLA LRYSILSEST PGSLSGTEQA EMKMAVISEH LGLSWAELAR ELQFSVEDIN RIRVENP NS LLEQSVALLN LWVIREGQNA NMENLYTALQ SIDRGEIVNM LEGSGRQSRN LKPDRRHTDR DYSLSPSQMN GYSSLQDE L LSPASLGCAL SSPLRADQYW NEVAVLDAIP LAATEHDTML EMSDMQVWSA GLTPSLVTAE DSSLECSKAE DSDATGHEW KLEGALSEEP RGPELGSLEL VEDDTVDSDA TNGLIDLLEQ EEGQRSEEKL PGSKRQDDAT GAGQDSENEV SLVSGHQRGQ ARITHSPTV SQVTERSQDR LQDWDADGSI VSYLQDAAQG SWQEEVTQGP HSFQGTSTMT EGLEPGGSQE YEKVLVSVSE H TWTEQPEA ESSQADRDRR QQGQEEQVQE AKNTFTQVVQ GNEFQNIPGE QVTEEQFTDE QGNIVTKKII RKVVRQIDLS SA DAAQEHE EVTVEGPLED PSELEVDIDY FMKHSKDHTS TPNP UniProtKB: Ankyrin-1 |
-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 |