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- EMDB-26952: Local refinement of ankyrin-1 (C-terminal half), class 1 of eryth... -

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Basic information

Entry
Database: EMDB / ID: EMD-26952
TitleLocal refinement of ankyrin-1 (C-terminal half), class 1 of erythrocyte ankyrin-1 complex
Map dataMain 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
  • Complex: Erythrocyte ankyrin-1 complex
    • Protein or peptide: Ankyrin-1
KeywordsMembrane 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 / ankyrin-1 complex / Neurofascin interactions / 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 / ankyrin-1 complex / Neurofascin interactions / 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 / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / Z disc / ATPase binding / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / transmembrane transporter binding / cytoskeleton / neuron projection / structural molecule activity / enzyme binding / signal transduction / plasma membrane / cytosol
Similarity search - Function
Ankyrin, UPA domain / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Ankyrin repeat / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain ...Ankyrin, UPA domain / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Ankyrin repeat / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Ankyrin repeats (many copies) / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsVallese F / Kim K / Yen LY / Johnston JD / Noble AJ / Cali T / Clarke OB
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionMay 11, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26952.png

Downloads & links

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Map

FileDownload / File: emd_26952.map.gz / Format: CCP4 / Size: 68.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map used for model building/refinement. Density modified and cropped with phenix.resolve_cryo_em, and resampled on fine grid with relion_image_handler.
Voxel sizeX=Y=Z: 0.415 Å
Density
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-4.510868 - 6.307402
Average (Standard dev.)0.00045345875 (±0.26350102)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions262262262
Spacing262262262
CellA=B=C: 108.729996 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Half map 1 (unmodified)

Fileemd_26952_additional_1.map
AnnotationHalf map 1 (unmodified)
Projections & Slices
AxesZYX

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Additional map: Half map 2 (unmodified)

Fileemd_26952_additional_2.map
AnnotationHalf map 2 (unmodified)
Projections & Slices
AxesZYX

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Additional map: Mask used for FSC calculation

Fileemd_26952_additional_3.map
AnnotationMask used for FSC calculation
Projections & Slices
AxesZYX

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Additional map: B-factor sharpened map.

Fileemd_26952_additional_4.map
AnnotationB-factor sharpened map.
Projections & Slices
AxesZYX

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Half map: Half map 1 (cropped and resampled to match main map).

Fileemd_26952_half_map_1.map
AnnotationHalf map 1 (cropped and resampled to match main map).
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 (cropped and resampled to match main map).

Fileemd_26952_half_map_2.map
AnnotationHalf map 2 (cropped and resampled to match main map).
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : Erythrocyte ankyrin-1 complex

EntireName: Erythrocyte ankyrin-1 complex
Components
  • Complex: Erythrocyte ankyrin-1 complex
    • Protein or peptide: Ankyrin-1

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Supramolecule #1: Erythrocyte ankyrin-1 complex

SupramoleculeName: 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.
Source (natural)Organism: Homo sapiens (human) / Organ: Blood / Tissue: Erythrocytes / Location in cell: Plasma membrane

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Macromolecule #1: Ankyrin-1

MacromoleculeName: Ankyrin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 206.522625 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 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.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 4-6 seconds, wait time 30 seconds..
DetailsAnkyrin complex mixture purified from digitonin-solubilized erythrocyte ghost membranes

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: Generated by stochastic gradient descent using ab intio reconstruction job type in cryoSPARC v3.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final 3D classificationDetails: Consensus refinement of erythrocyte ankyrin-1 complexes
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 126197
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4yzf


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7v0x:
Local refinement of ankyrin-1 (C-terminal half), class 1 of erythrocyte ankyrin-1 complex

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