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- EMDB-26972: Local refinement of Anykyrin-1 (N-terminal half of membrane bindi... -

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Entry
Database: EMDB / ID: EMD-26972
TitleLocal refinement of Anykyrin-1 (N-terminal half of membrane binding domain) in Class 2 of erythrocyte ankyrin-1 complex
Map dataMain map used for model fitting. Density modified and cropped using phenix.resolve_cryo_em, resampled on fine grid using relion_image_handler.
Sample
  • Complex: Class 2 of the erythrocyte ankyrin-1 complex (local refinement of N-terminal half of membrane binding domain, bound to N-terminal peptide of band3)
    • Protein or peptide: Ankyrin-1
    • Protein or peptide: Band 3 anion transport protein
  • Ligand: water
KeywordsMembrane Protein / Anion Exchange / Erythrocyte / Glycoprotein / TRANSPORT PROTEIN-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


spectrin-associated cytoskeleton / positive regulation of organelle organization / 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 / Neurofascin interactions / Bicarbonate transporters / intracellular monoatomic ion homeostasis ...spectrin-associated cytoskeleton / positive regulation of organelle organization / 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 / Neurofascin interactions / Bicarbonate transporters / intracellular monoatomic ion homeostasis / ankyrin-1 complex / CHL1 interactions / monoatomic anion transmembrane transporter activity / plasma membrane phospholipid scrambling / cytoskeletal anchor activity / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / monoatomic anion transport / M band / chloride transport / chloride transmembrane transporter activity / Interaction between L1 and Ankyrins / ankyrin binding / hemoglobin binding / spectrin binding / negative regulation of glycolytic process through fructose-6-phosphate / erythrocyte development / cortical cytoskeleton / exocytosis / axolemma / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / protein-membrane adaptor activity / cytoskeleton organization / chloride transmembrane transport / sarcoplasmic reticulum / regulation of intracellular pH / protein localization to plasma membrane / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / sarcolemma / structural constituent of cytoskeleton / transmembrane transport / cytoplasmic side of plasma membrane / Z disc / blood coagulation / ATPase binding / protein phosphatase binding / blood microparticle / basolateral plasma membrane / transmembrane transporter binding / postsynaptic membrane / cytoskeleton / neuron projection / structural molecule activity / enzyme binding / signal transduction / protein homodimerization activity / extracellular exosome / membrane / 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. / Anion exchange protein 1 / Anion exchange protein / Anion exchange, conserved site ...Ankyrin, UPA domain / UPA domain / : / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Anion exchange protein 1 / Anion exchange protein / Anion exchange, conserved site / Anion exchangers family signature 1. / Anion exchangers family signature 2. / Band 3 cytoplasmic domain / Band 3 cytoplasmic domain / Phosphotransferase/anion transporter / Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter integral membrane domain / Ankyrin repeat / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / 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
Band 3 anion transport protein / Ankyrin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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 13, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26972.png

Downloads & links

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Map

FileDownload / File: emd_26972.map.gz / Format: CCP4 / Size: 109.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map used for model fitting. Density modified and cropped using phenix.resolve_cryo_em, resampled on fine grid using relion_image_handler.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.42 Å/pix.
x 306 pix.
= 126.99 Å		0.42 Å/pix.
x 306 pix.
= 126.99 Å		0.42 Å/pix.
x 306 pix.
= 126.99 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.415 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-4.5268974 - 6.209984
Average (Standard dev.)0.00026899696 (±0.22702178)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions306306306
Spacing306306306
CellA=B=C: 126.99 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Half map 2 (unmodified)

Fileemd_26972_additional_1.map
AnnotationHalf map 2 (unmodified)
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Additional map: Half map 1 (unmodified)

Fileemd_26972_additional_2.map
AnnotationHalf map 1 (unmodified)
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Additional map: Mask used for FSC calculation

Fileemd_26972_additional_3.map
AnnotationMask used for FSC calculation
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Additional map: B-factor sharpened map.

Fileemd_26972_additional_4.map
AnnotationB-factor sharpened map.
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Half map: Half map 1 (cropped and resampled)

Fileemd_26972_half_map_1.map
AnnotationHalf map 1 (cropped and resampled)
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AxesZYX

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Slices (1/2)
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Histogram

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Half map: Half map 2 (cropped and resampled)

Fileemd_26972_half_map_2.map
AnnotationHalf map 2 (cropped and resampled)
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Sample components

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Entire : Class 2 of the erythrocyte ankyrin-1 complex (local refinement of...

EntireName: Class 2 of the erythrocyte ankyrin-1 complex (local refinement of N-terminal half of membrane binding domain, bound to N-terminal peptide of band3)
Components
  • Complex: Class 2 of the erythrocyte ankyrin-1 complex (local refinement of N-terminal half of membrane binding domain, bound to N-terminal peptide of band3)
    • Protein or peptide: Ankyrin-1
    • Protein or peptide: Band 3 anion transport protein
  • Ligand: water

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Supramolecule #1: Class 2 of the erythrocyte ankyrin-1 complex (local refinement of...

SupramoleculeName: Class 2 of the erythrocyte ankyrin-1 complex (local refinement of N-terminal half of membrane binding domain, bound to N-terminal peptide of band3)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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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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Macromolecule #2: Band 3 anion transport protein

MacromoleculeName: Band 3 anion transport protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 101.883859 KDa
SequenceString: MEELQDDYED MMEENLEQEE YEDPDIPESQ MEEPAAHDTE ATATDYHTTS HPGTHKVYVE LQELVMDEKN QELRWMEAAR WVQLEENLG ENGAWGRPHL SHLTFWSLLE LRRVFTKGTV LLDLQETSLA GVANQLLDRF IFEDQIRPQD REELLRALLL K HSHAGELE ...String:
MEELQDDYED MMEENLEQEE YEDPDIPESQ MEEPAAHDTE ATATDYHTTS HPGTHKVYVE LQELVMDEKN QELRWMEAAR WVQLEENLG ENGAWGRPHL SHLTFWSLLE LRRVFTKGTV LLDLQETSLA GVANQLLDRF IFEDQIRPQD REELLRALLL K HSHAGELE ALGGVKPAVL TRSGDPSQPL LPQHSSLETQ LFCEQGDGGT EGHSPSGILE KIPPDSEATL VLVGRADFLE QP VLGFVRL QEAAELEAVE LPVPIRFLFV LLGPEAPHID YTQLGRAAAT LMSERVFRID AYMAQSRGEL LHSLEGFLDC SLV LPPTDA PSEQALLSLV PVQRELLRRR YQSSPAKPDS SFYKGLDLNG GPDDPLQQTG QLFGGLVRDI RRRYPYYLSD ITDA FSPQV LAAVIFIYFA ALSPAITFGG LLGEKTRNQM GVSELLISTA VQGILFALLG AQPLLVVGFS GPLLVFEEAF FSFCE TNGL EYIVGRVWIG FWLILLVVLV VAFEGSFLVR FISRYTQEIF SFLISLIFIY ETFSKLIKIF QDHPLQKTYN YNVLMV PKP QGPLPNTALL SLVLMAGTFF FAMMLRKFKN SSYFPGKLRR VIGDFGVPIS ILIMVLVDFF IQDTYTQKLS VPDGFKV SN SSARGWVIHP LGLRSEFPIW MMFASALPAL LVFILIFLES QITTLIVSKP ERKMVKGSGF HLDLLLVVGM GGVAALFG M PWLSATTVRS VTHANALTVM GKASTPGAAA QIQEVKEQRI SGLLVAVLVG LSILMEPILS RIPLAVLFGI FLYMGVTSL SGIQLFDRIL LLFKPPKYHP DVPYVKRVKT WRMHLFTGIQ IICLAVLWVV KSTPASLALP FVLILTVPLR RVLLPLIFRN VELQCLDAD DAKATFDEEE GRDEYDEVAM PV

UniProtKB: Band 3 anion transport protein

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 48 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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

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Image processing

CTF correctionDetails: Patch CTF (cryoSPARC v3) followed by per particle defocus refinement and refinement of higher order aberrations (cryoSPARC v3)
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Generated by stochastic gradient descent using ab intio reconstruction job type in cryoSPARC v3.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 145645
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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