[English] 日本語
Yorodumi
- EMDB-26154: Cryo-EM structure of human ankyrin complex (B2P1A1)2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26154
TitleCryo-EM structure of human ankyrin complex (B2P1A1)2
Map dataCryo-EM structure of Ankyrin complex (B2P1A1)2
Sample
  • Complex: High-salt fraction 2 from human red blood cell membrane
    • Protein or peptide: band 3Band 3 anion transport protein
    • Protein or peptide: protein 4.2
    • Protein or peptide: ankyrin
KeywordsRed blood cell / Ankyrin complex / membrane protein / band 3 / protein 4.2
Function / homology
Function and homology information


hemoglobin metabolic process / spectrin-associated cytoskeleton / positive regulation of organelle organization / protein-glutamine gamma-glutamyltransferase activity / 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 ...hemoglobin metabolic process / spectrin-associated cytoskeleton / positive regulation of organelle organization / protein-glutamine gamma-glutamyltransferase activity / 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 transmembrane transporter activity / chloride transport / erythrocyte development / negative regulation of glycolytic process through fructose-6-phosphate / ankyrin binding / spectrin binding / hemoglobin binding / cortical cytoskeleton / exocytosis / erythrocyte maturation / axolemma / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / protein-membrane adaptor activity / spleen development / chloride transmembrane transport / cytoskeleton organization / sarcoplasmic reticulum / protein localization to plasma membrane / regulation of intracellular pH / sarcolemma / cell morphogenesis / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / transmembrane transport / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / Z disc / multicellular organismal-level iron ion homeostasis / blood coagulation / ATPase binding / regulation of cell shape / 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 / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
Ankyrin, UPA domain / UPA domain / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. ...Ankyrin, UPA domain / UPA domain / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Anion exchange protein 1 / Transglutaminase-like superfamily / 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 / 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 / Papain-like cysteine peptidase superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Band 3 anion transport protein / Ankyrin-1 / Protein 4.2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsXia X / Liu SH / Zhou ZH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01GM071940 United States
CitationJournal: 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
DepositionFeb 6, 2022-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26154.png

Downloads & links

-
Map

FileDownload / File: emd_26154.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Ankyrin complex (B2P1A1)2
Voxel sizeX=Y=Z: 2.2 Å
Density
Contour LevelBy AUTHOR: 0.73
Minimum - Maximum-0.27127674 - 1.8833799
Average (Standard dev.)0.005167456 (±0.09649133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 616.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : High-salt fraction 2 from human red blood cell membrane

EntireName: High-salt fraction 2 from human red blood cell membrane
Components
  • Complex: High-salt fraction 2 from human red blood cell membrane
    • Protein or peptide: band 3Band 3 anion transport protein
    • Protein or peptide: protein 4.2
    • Protein or peptide: ankyrin

-
Supramolecule #1: High-salt fraction 2 from human red blood cell membrane

SupramoleculeName: High-salt fraction 2 from human red blood cell membrane
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1 MDa

-
Macromolecule #1: band 3

MacromoleculeName: band 3 / type: protein_or_peptide / ID: 1 / Details: four band 3 in the complex / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MEELQDDYED MMEENLEQEE YEDPDIPESQ MEEPAAHDTE ATATDYHTTS HPGTHKVYVE LQELVMDEKN QELRWMEAAR WVQLEENLGE NGAWGRPHLS HLTFWSLLEL RRVFTKGTVL LDLQETSLAG VANQLLDRFI FEDQIRPQDR EELLRALLLK HSHAGELEAL ...String:
MEELQDDYED MMEENLEQEE YEDPDIPESQ MEEPAAHDTE ATATDYHTTS HPGTHKVYVE LQELVMDEKN QELRWMEAAR WVQLEENLGE NGAWGRPHLS HLTFWSLLEL RRVFTKGTVL LDLQETSLAG VANQLLDRFI FEDQIRPQDR EELLRALLLK HSHAGELEAL GGVKPAVLTR SGDPSQPLLP QHSSLETQLF CEQGDGGTEG HSPSGILEKI PPDSEATLVL VGRADFLEQP VLGFVRLQEA AELEAVELPV PIRFLFVLLG PEAPHIDYTQ LGRAAATLMS ERVFRIDAYM AQSRGELLHS LEGFLDCSLV LPPTDAPSEQ ALLSLVPVQR ELLRRRYQSS PAKPDSSFYK GLDLNGGPDD PLQQTGQLFG GLVRDIRRRY PYYLSDITDA FSPQVLAAVI FIYFAALSPA ITFGGLLGEK TRNQMGVSEL LISTAVQGIL FALLGAQPLL VVGFSGPLLV FEEAFFSFCE TNGLEYIVGR VWIGFWLILL VVLVVAFEGS FLVRFISRYT QEIFSFLISL IFIYETFSKL IKIFQDHPLQ KTYNYNVLMV PKPQGPLPNT ALLSLVLMAG TFFFAMMLRK FKNSSYFPGK LRRVIGDFGV PISILIMVLV DFFIQDTYTQ KLSVPDGFKV SNSSARGWVI HPLGLRSEFP IWMMFASALP ALLVFILIFL ESQITTLIVS KPERKMVKGS GFHLDLLLVV GMGGVAALFG MPWLSATTVR SVTHANALTV MGKASTPGAA AQIQEVKEQR ISGLLVAVLV GLSILMEPIL SRIPLAVLFG IFLYMGVTSL SGIQLFDRIL LLFKPPKYHP DVPYVKRVKT WRMHLFTGIQ IICLAVLWVV KSTPASLALP FVLILTVPLR RVLLPLIFRN VELQCLDADD AKATFDEEEG RDEYDEVAMP V

UniProtKB: Band 3 anion transport protein

-
Macromolecule #2: protein 4.2

MacromoleculeName: protein 4.2 / type: protein_or_peptide / ID: 2 / Details: two protein 4.2 in the complex / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MGQALGIKSC DFQAARNNEE HHTKALSSRR LFVRRGQPFT IILYFRAPVR AFLPALKKVA LTAQTGEQPS KINRTQATFP ISSLGDRKWW SAVVEERDAQ SWTISVTTPA DAVIGHYSLL LQVSGRKQLL LGQFTLLFNP WNREDAVFLK NEAQRMEYLL NQNGLIYLGT ...String:
MGQALGIKSC DFQAARNNEE HHTKALSSRR LFVRRGQPFT IILYFRAPVR AFLPALKKVA LTAQTGEQPS KINRTQATFP ISSLGDRKWW SAVVEERDAQ SWTISVTTPA DAVIGHYSLL LQVSGRKQLL LGQFTLLFNP WNREDAVFLK NEAQRMEYLL NQNGLIYLGT ADCIQAESWD FGQFEGDVID LSLRLLSKDK QVEKWSQPVH VARVLGALLH FLKEQRVLPT PQTQATQEGA LLNKRRGSVP ILRQWLTGRG RPVYDGQAWV LAAVACTVLR CLGIPARVVT TFASAQGTGG RLLIDEYYNE EGLQNGEGQR GRIWIFQTST ECWMTRPALP QGYDGWQILH PSAPNGGGVL GSCDLVPVRA VKEGTLGLTP AVSDLFAAIN ASCVVWKCCE DGTLELTDSN TKYVGNNIST KGVGSDRCED ITQNYKYPEG SLQEKEVLER VEKEKMEREK DNGIRPPSLE TASPLYLLLK APSSLPLRGD AQISVTLVNH SEQEKAVQLA IGVQAVHYNG VLAAKLWRKK LHLTLSANLE KIITIGLFFS NFERNPPENT FLRLTAMATH SESNLSCFAQ EDIAICRPHL AIKMPEKAEQ YQPLTASVSL QNSLDAPMED CVISILGRGL IHRERSYRFR SVWPENTMCA KFQFTPTHVG LQRLTVEVDC NMFQNLTNYK SVTVVAPELS A

UniProtKB: Protein 4.2

-
Macromolecule #3: ankyrin

MacromoleculeName: ankyrin / type: protein_or_peptide / ID: 3 / Details: two ankyrin in the complex / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MPYSVGFREA DAATSFLRAA RSGNLDKALD HLRNGVDINT CNQNGLNGLH LASKEGHVKM VVELLHKEII LETTTKKGNT ALHIAALAGQ DEVVRELVNY GANVNAQSQK GFTPLYMAAQ ENHLEVVKFL LENGANQNVA TEDGFTPLAV ALQQGHENVV AHLINYGTKG ...String:
MPYSVGFREA DAATSFLRAA RSGNLDKALD HLRNGVDINT CNQNGLNGLH LASKEGHVKM VVELLHKEII LETTTKKGNT ALHIAALAGQ DEVVRELVNY GANVNAQSQK GFTPLYMAAQ ENHLEVVKFL LENGANQNVA TEDGFTPLAV ALQQGHENVV AHLINYGTKG KVRLPALHIA ARNDDTRTAA VLLQNDPNPD VLSKTGFTPL HIAAHYENLN VAQLLLNRGA SVNFTPQNGI TPLHIASRRG NVIMVRLLLD RGAQIETKTK DELTPLHCAA RNGHVRISEI LLDHGAPIQA KTKNGLSPIH MAAQGDHLDC VRLLLQYDAE IDDITLDHLT PLHVAAHCGH HRVAKVLLDK GAKPNSRALN GFTPLHIACK KNHVRVMELL LKTGASIDAV TESGLTPLHV ASFMGHLPIV KNLLQRGASP NVSNVKVETP LHMAARAGHT EVAKYLLQNK AKVNAKAKDD QTPLHCAARI GHTNMVKLLL ENNANPNLAT TAGHTPLHIA AREGHVETVL ALLEKEASQA CMTKKGFTPL HVAAKYGKVR VAELLLERDA HPNAAGKNGL TPLHVAVHHN NLDIVKLLLP RGGSPHSPAW NGYTPLHIAA KQNQVEVARS LLQYGGSANA ESVQGVTPLH LAAQEGHAEM VALLLSKQAN GNLGNKSGLT PLHLVAQEGH VPVADVLIKH GVMVDATTRM GYTPLHVASH YGNIKLVKFL LQHQADVNAK TKLGYSPLHQ AAQQGHTDIV TLLLKNGASP NEVSSDGTTP LAIAKRLGYI SVTDVLKVVT DETSFVLVSD KHRMSFPETV DEILDVSEDE GEELISFKAE RRDSRDVDEE KELLDFVPKL DQVVESPAIP RIPCAMPETV VIRSEEQEQA SKEYDEDSLI PSSPATETSD NISPVASPVH TGFLVSFMVD ARGGSMRGSR HNGLRVVIPP RTCAAPTRIT CRLVKPQKLS TPPPLAEEEG LASRIIALGP TGAQFLSPVI VEIPHFASHG RGDRELVVLR SENGSVWKEH RSRYGESYLD QILNGMDEEL GSLEELEKKR VCRIITTDFP LYFVIMSRLC QDYDTIGPEG GSLKSKLVPL VQATFPENAV TKRVKLALQA QPVPDELVTK LLGNQATFSP IVTVEPRRRK FHRPIGLRIP LPPSWTDNPR DSGEGDTTSL RLLCSVIGGT DQAQWEDITG TTKLVYANEC ANFTTNVSAR FWLSDCPRTA EAVNFATLLY KELTAVPYMA KFVIFAKMND PREGRLRCYC MTDDKVDKTL EQHENFVEVA RSRDIEVLEG MSLFAELSGN LVPVKKAAQQ RSFHFQSFRE NRLAMPVKVR DSSREPGGSL SFLRKAMKYE DTQHILCHLN ITMPPCAKGS GAEDRRRTPT PLALRYSILS ESTPGSLSGT EQAEMKMAVI SEHLGLSWAE LARELQFSVE DINRIRVENP NSLLEQSVAL LNLWVIREGQ NANMENLYTA LQSIDRGEIV NMLEGSGRQS RNLKPDRRHT DRDYSLSPSQ MNGYSSLQDE LLSPASLGCA LSSPLRADQY WNEVAVLDAI PLAATEHDTM LEMSDMQVWS AGLTPSLVTA EDSSLECSKA EDSDATGHEW KLEGALSEEP RGPELGSLEL VEDDTVDSDA TNGLIDLLEQ EEGQRSEEKL PGSKRQDDAT GAGQDSENEV SLVSGHQRGQ ARITHSPTVS QVTERSQDRL QDWDADGSIV SYLQDAAQGS WQEEVTQGPH SFQGTSTMTE GLEPGGSQEY EKVLVSVSEH TWTEQPEAES SQADRDRRQQ GQEEQVQEAK NTFTQVVQGN EFQNIPGEQV TEEQFTDEQG NIVTKKIIRK VVRQIDLSSA DAAQEHEEVT VEGPLEDPSE LEVDIDYFMK HSKDHTSTPN P

UniProtKB: Ankyrin-1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMNH2C(CH2OH)3HClTris-HClTris
300.0 mMNaClSodium chlorideSodium Chloride
1.0 mMHSCH2CH(OH)CH(OH)CH2SHDTT
0.015 %C24H46O11DDM
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 100.0 K / Max: 100.0 K
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 15351225
Startup modelType of model: NONE / Details: Generated from CryoSPARC
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 26826

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

+
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