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- PDB-8cs9: Composite reconstruction of Class 1 of the erythrocyte ankyrin-1 ... -

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Basic information

Entry
Database: PDB / ID: 8cs9
TitleComposite reconstruction of Class 1 of the erythrocyte ankyrin-1 complex
Components
  • Ammonium transporter Rh type A
  • Ankyrin-1
  • Band 3 anion transport protein
  • Blood group Rh(CE) polypeptide
  • Glycophorin-A
  • Glycophorin-B
  • Protein 4.2
KeywordsTRANSPORT PROTEIN/STRUCTURAL PROTEIN / Membrane Protein / Anion Exchange / Erythrocyte / Glycoprotein / TRANSPORT PROTEIN-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


methylammonium transmembrane transport / Defective RHAG causes regulator type Rh-null hemolytic anemia (RHN) / Rhesus blood group biosynthesis / methylammonium transmembrane transporter activity / Rhesus glycoproteins mediate ammonium transport. / ammonium homeostasis / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / hemoglobin metabolic process / spectrin-associated cytoskeleton ...methylammonium transmembrane transport / Defective RHAG causes regulator type Rh-null hemolytic anemia (RHN) / Rhesus blood group biosynthesis / methylammonium transmembrane transporter activity / Rhesus glycoproteins mediate ammonium transport. / ammonium homeostasis / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / 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 / ammonium transmembrane transport / Defective SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA) / leak channel activity / 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 / ammonium channel activity / solute:inorganic anion antiporter activity / cytoskeletal anchor activity / bicarbonate transmembrane transporter activity / bicarbonate transport / monoatomic anion transport / M band / inorganic cation transmembrane transport / 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 / Cell surface interactions at the vascular wall / sarcolemma / carbon dioxide transport / 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 / virus receptor activity / 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 / nucleoplasm / ATP binding / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Blood group Rhesus C/E/D polypeptide / Glycophorin, conserved site / : / Glycophorin A / Glycophorin A signature. / Glycophorin / Ankyrin, UPA domain / UPA domain / Transglutaminase, N-terminal / Transglutaminase, C-terminal ...Blood group Rhesus C/E/D polypeptide / Glycophorin, conserved site / : / Glycophorin A / Glycophorin A signature. / Glycophorin / 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. / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter / 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 / 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 / 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
CHOLESTEROL / Chem-PIO / Glycophorin-A / Band 3 anion transport protein / Glycophorin-B / Ankyrin-1 / Protein 4.2 / Blood group Rh(CE) polypeptide / Ammonium transporter Rh type A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsVallese, F. / Kim, K. / Yen, L.Y. / Johnston, J.D. / Noble, A.J. / Cali, T. / Clarke, O.B.
Funding support1items
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 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ankyrin-1
K: Blood group Rh(CE) polypeptide
L: Ammonium transporter Rh type A
Q: Ammonium transporter Rh type A
X: Protein 4.2
P: Glycophorin-B
R: Glycophorin-A
a: Glycophorin-A
V: Band 3 anion transport protein
e: Band 3 anion transport protein
S: Glycophorin-A
b: Glycophorin-A
Y: Band 3 anion transport protein
f: Band 3 anion transport protein
T: Glycophorin-A
c: Glycophorin-A
Z: Band 3 anion transport protein
g: Band 3 anion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,148,26442
Polymers1,136,86118
Non-polymers11,40224
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 7 types, 18 molecules AKLQXPRaSbTcVeYfZg

#1: Protein Ankyrin-1 / / ANK-1 / Ankyrin-R / Erythrocyte ankyrin


Mass: 206522.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P16157
#2: Protein Blood group Rh(CE) polypeptide / Rh polypeptide 1 / RhPI / Rh30A / RhIXB / Rhesus C/E antigens


Mass: 45598.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18577
#3: Protein Ammonium transporter Rh type A / Erythrocyte membrane glycoprotein Rh50 / Erythrocyte plasma membrane 50 kDa glycoprotein / Rh50A / ...Erythrocyte membrane glycoprotein Rh50 / Erythrocyte plasma membrane 50 kDa glycoprotein / Rh50A / Rhesus blood group family type A glycoprotein / Rh family type A glycoprotein / Rh type A glycoprotein / Rhesus blood group-associated ammonia channel / Rhesus blood group-associated glycoprotein


Mass: 44229.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02094
#4: Protein Protein 4.2 / / P4.2 / Erythrocyte membrane protein band 4.2 / Erythrocyte protein 4.2


Mass: 77096.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P16452
#5: Protein Glycophorin-B / PAS-3 / SS-active sialoglycoprotein / Sialoglycoprotein delta


Mass: 9789.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P06028
#6: Protein
Glycophorin-A / MN sialoglycoprotein / PAS-2 / Sialoglycoprotein alpha


Mass: 16348.433 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02724
#7: Protein
Band 3 anion transport protein / / Anion exchange protein 1 / AE 1 / Anion exchanger 1 / Solute carrier family 4 member 1


Mass: 101883.859 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02730

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Sugars , 2 types, 9 molecules

#8: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#11: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 283 molecules

#9: Chemical
ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H46O
#10: Chemical ChemComp-AJP / Digitonin / Digitonin


Mass: 1229.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H92O29 / Comment: detergent*YM
#12: Chemical
ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Class 1 of erythrocyte ankyrin complex (composite map)
Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 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.
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Ankyrin complex mixture purified from digitonin-solubilized erythrocyte ghost membranes
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 4-6 seconds, wait time 30 seconds

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 14464 / Details: Two grids were imaged in a single session.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameCategory
2Leginonimage acquisition
13cryoSPARC3D reconstruction
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
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126197 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00762061
ELECTRON MICROSCOPYf_angle_d0.82884375
ELECTRON MICROSCOPYf_dihedral_angle_d8.5788530
ELECTRON MICROSCOPYf_chiral_restr0.0449969
ELECTRON MICROSCOPYf_plane_restr0.00610479

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