[English] 日本語
Yorodumi
- EMDB-26918: Ankyrin-1 (N-terminal region of membrane binding domain, local re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26918
TitleAnkyrin-1 (N-terminal region of membrane binding domain, local refinement from consensus reconstruction; bound to N-terminal peptide from band 3)
Map dataMain map used for model building/refinement. Density modified and cropped using phenix.resolve_cryo_em, then resampled on a finer grid with relion_image_handler.
Sample
  • Complex: Ankyrin complex mixture purified from digitonin-solubilized erythrocyte ghost membranes
    • Protein or peptide: Ankyrin-1
    • Protein or peptide: Band 3 anion transport protein
  • Ligand: water
KeywordsMembrane Protein / Erythrocyte / Ankyrin / STRUCTURAL PROTEIN
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 / Bicarbonate transporters / intracellular monoatomic ion homeostasis / ankyrin-1 complex ...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 / Bicarbonate transporters / intracellular monoatomic ion homeostasis / ankyrin-1 complex / Neurofascin interactions / plasma membrane phospholipid scrambling / CHL1 interactions / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / cytoskeletal anchor activity / bicarbonate transmembrane transporter activity / bicarbonate transport / monoatomic anion transport / M band / Interaction between L1 and Ankyrins / chloride transport / chloride transmembrane transporter activity / erythrocyte development / negative regulation of glycolytic process through fructose-6-phosphate / ankyrin binding / spectrin binding / hemoglobin binding / 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 / protein localization to plasma membrane / regulation of intracellular pH / sarcolemma / transmembrane transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / Z disc / blood coagulation / ATPase binding / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / blood microparticle / transmembrane transporter binding / 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 / Anion exchangers family signature 1. ...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 / Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter family / Phosphotransferase/anion transporter / 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
Band 3 anion transport protein / Ankyrin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 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 9, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26918.png

Downloads & links

-
Map

FileDownload / File: emd_26918.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map used for model building/refinement. Density modified and cropped using phenix.resolve_cryo_em, then resampled on a finer grid with relion_image_handler.
Voxel sizeX=Y=Z: 0.415 Å
Density
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-4.592819 - 6.569179
Average (Standard dev.)0.0004000316 (±0.2825912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 119.52 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Mask used for FSC calculation.

Fileemd_26918_additional_1.map
AnnotationMask used for FSC calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half map 1 (unmodified)

Fileemd_26918_additional_2.map
AnnotationHalf map 1 (unmodified)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half map 2 (unmodified)

Fileemd_26918_additional_3.map
AnnotationHalf map 2 (unmodified)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened map (B=65.5).

Fileemd_26918_additional_4.map
AnnotationSharpened map (B=65.5).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 (cropped and resampled)

Fileemd_26918_half_map_1.map
AnnotationHalf map 2 (cropped and resampled)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 (cropped and resampled)

Fileemd_26918_half_map_2.map
AnnotationHalf map 1 (cropped and resampled)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ankyrin complex mixture purified from digitonin-solubilized eryth...

EntireName: Ankyrin complex mixture purified from digitonin-solubilized erythrocyte ghost membranes
Components
  • Complex: Ankyrin complex mixture purified from digitonin-solubilized erythrocyte ghost membranes
    • Protein or peptide: Ankyrin-1
    • Protein or peptide: Band 3 anion transport protein
  • Ligand: water

-
Supramolecule #1: Ankyrin complex mixture purified from digitonin-solubilized eryth...

SupramoleculeName: Ankyrin complex mixture purified from digitonin-solubilized erythrocyte ghost membranes
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: N-terminal part of ankyrin-1 membrane binding domain (local refinement) bound to N-terminal fragment of band 3
Source (natural)Organism: Homo sapiens (human) / Organ: Blood / Tissue: Erythrocytes / Location in cell: Plasma membrane

-
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) / Organ: Blood / Tissue: Erythrocytes
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

-
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) / Organ: Blood / Tissue: Erythrocytes
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

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 79 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

-
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: This corresponds to a class of band 3-GPA particles isolated from a mixture mostly consisting of ankyrin complexes.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 710437
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7uzu:
Ankyrin-1 (N-terminal region of membrane binding domain, local refinement from consensus reconstruction; bound to N-terminal peptide from band 3)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more