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- EMDB-26149: Cryo-EM structure of human ankyrin complex (B2P1A1) from red bloo... -
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Basic information
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Title | Cryo-EM structure of human ankyrin complex (B2P1A1) from red blood cell | |||||||||
![]() | Cryo-EM structure of B2P1A1 | |||||||||
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![]() | Red blood cell / Ankyrin complex / membrane protein / band 3 / protein 4.2 | |||||||||
Function / homology | ![]() 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 / Neurofascin interactions / intracellular monoatomic ion homeostasis / ankyrin-1 complex / plasma membrane phospholipid scrambling / CHL1 interactions / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / cytoskeletal anchor activity / solute:inorganic anion antiporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / monoatomic anion transport / M band / Interaction between L1 and Ankyrins / chloride transport / chloride transmembrane transporter activity / ankyrin binding / negative regulation of glycolytic process through fructose-6-phosphate / spectrin binding / hemoglobin binding / cortical cytoskeleton / exocytosis / erythrocyte maturation / axolemma / erythrocyte development / 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 / cell morphogenesis / 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 / transmembrane transport / sarcolemma / multicellular organismal-level iron ion homeostasis / Z disc / blood coagulation / regulation of cell shape / ATPase binding / basolateral plasma membrane / postsynaptic membrane / protein phosphatase binding / transmembrane transporter binding / blood microparticle / cytoskeleton / neuron projection / structural molecule activity / enzyme binding / signal transduction / protein homodimerization activity / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
![]() | Xia X / Liu SH | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 203.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.5 KB 19.5 KB | Display Display | ![]() |
Images | ![]() | 123 KB | ||
Filedesc metadata | ![]() | 7.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 468.8 KB | Display | ![]() |
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Full document | ![]() | 468.4 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tw3MC ![]() 7tvzC ![]() 7tw0C ![]() 7tw1C ![]() 7tw2C ![]() 7tw5C ![]() 7tw6C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM structure of B2P1A1 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : High-salt fraction 2 from human red blood cell membrane
Entire | Name: High-salt fraction 2 from human red blood cell membrane |
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Components |
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-Supramolecule #1: High-salt fraction 2 from human red blood cell membrane
Supramolecule | Name: High-salt fraction 2 from human red blood cell membrane type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 480 KDa |
-Macromolecule #1: Band 3 anion transport protein
Macromolecule | Name: Band 3 anion transport protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 101.883859 KDa |
Sequence | String: 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 #2: Protein 4.2
Macromolecule | Name: Protein 4.2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 77.096914 KDa |
Sequence | String: MGQALGIKSC DFQAARNNEE HHTKALSSRR LFVRRGQPFT IILYFRAPVR AFLPALKKVA LTAQTGEQPS KINRTQATFP ISSLGDRKW WSAVVEERDA QSWTISVTTP ADAVIGHYSL LLQVSGRKQL LLGQFTLLFN PWNREDAVFL KNEAQRMEYL L NQNGLIYL ...String: MGQALGIKSC DFQAARNNEE HHTKALSSRR LFVRRGQPFT IILYFRAPVR AFLPALKKVA LTAQTGEQPS KINRTQATFP ISSLGDRKW WSAVVEERDA QSWTISVTTP ADAVIGHYSL LLQVSGRKQL LLGQFTLLFN PWNREDAVFL KNEAQRMEYL L NQNGLIYL GTADCIQAES WDFGQFEGDV IDLSLRLLSK DKQVEKWSQP VHVARVLGAL LHFLKEQRVL PTPQTQATQE GA LLNKRRG SVPILRQWLT GRGRPVYDGQ AWVLAAVACT VLRCLGIPAR VVTTFASAQG TGGRLLIDEY YNEEGLQNGE GQR GRIWIF QTSTECWMTR PALPQGYDGW QILHPSAPNG GGVLGSCDLV PVRAVKEGTL GLTPAVSDLF AAINASCVVW KCCE DGTLE LTDSNTKYVG NNISTKGVGS DRCEDITQNY KYPEGSLQEK EVLERVEKEK MEREKDNGIR PPSLETASPL YLLLK APSS LPLRGDAQIS VTLVNHSEQE KAVQLAIGVQ AVHYNGVLAA KLWRKKLHLT LSANLEKIIT IGLFFSNFER NPPENT FLR LTAMATHSES NLSCFAQEDI AICRPHLAIK MPEKAEQYQP LTASVSLQNS LDAPMEDCVI SILGRGLIHR ERSYRFR SV WPENTMCAKF QFTPTHVGLQ RLTVEVDCNM FQNLTNYKSV TVVAPELSA UniProtKB: Protein 4.2 |
-Macromolecule #3: Ankyrin-1
Macromolecule | Name: Ankyrin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.5 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 100.0 K / Max: 100.0 K |
Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 81000 |
Sample stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 214 |
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Output model | ![]() PDB-7tw3: |