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- EMDB-26916: Local refinement of RhAG-RhCE-ANK1(AR1-5), from consensus refinem... -

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Basic information

Entry
Database: EMDB / ID: EMD-26916
TitleLocal refinement of RhAG-RhCE-ANK1(AR1-5), from consensus refinement of all classes
Map dataMain map used for model building/refinement. Density modified and cropped using phenix.resolve_cryo_em, resampled on fine grid using relion_image_handler.
Sample
  • Complex: Ankyrin complex mixture purified from digitonin-solubilized erythrocyte ghost membranes
    • Protein or peptide: Blood group Rh(CE) polypeptide
    • Protein or peptide: Ammonium transporter Rh type A
    • Protein or peptide: Ankyrin-1
  • Ligand: CHOLESTEROL
  • Ligand: Digitonin
  • Ligand: water
KeywordsMembrane Protein / Anion Exchange / Erythrocyte / Glycoprotein / TRANSPORT PROTEIN
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 / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / ammonium homeostasis / spectrin-associated cytoskeleton / positive regulation of organelle organization ...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 / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / ammonium homeostasis / spectrin-associated cytoskeleton / positive regulation of organelle organization / leak channel activity / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / Neurofascin interactions / ammonium transmembrane transport / intracellular monoatomic ion homeostasis / ammonium channel activity / ankyrin-1 complex / CHL1 interactions / cytoskeletal anchor activity / bicarbonate transport / M band / inorganic cation transmembrane transport / Interaction between L1 and Ankyrins / ankyrin binding / spectrin binding / exocytosis / axolemma / endoplasmic reticulum to Golgi vesicle-mediated transport / erythrocyte development / COPI-mediated anterograde transport / cytoskeleton organization / sarcoplasmic reticulum / protein localization to plasma membrane / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / sarcolemma / structural constituent of cytoskeleton / Z disc / multicellular organismal-level iron ion homeostasis / cytoplasmic side of plasma membrane / ATPase binding / basolateral plasma membrane / protein phosphatase binding / postsynaptic membrane / transmembrane transporter binding / cytoskeleton / neuron projection / structural molecule activity / enzyme binding / signal transduction / membrane / plasma membrane / cytosol
Similarity search - Function
Blood group Rhesus C/E/D polypeptide / Ankyrin, UPA domain / UPA domain / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. ...Blood group Rhesus C/E/D polypeptide / Ankyrin, UPA domain / UPA domain / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / 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
Ankyrin-1 / Blood group Rh(CE) polypeptide / Ammonium transporter Rh type A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.17 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

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Structure visualization

Supplemental images

emd_26916.png

Downloads & links

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Map

FileDownload / File: emd_26916.map.gz / Format: CCP4 / Size: 71.8 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, 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 266 pix.
= 110.39 Å		0.42 Å/pix.
x 266 pix.
= 110.39 Å		0.42 Å/pix.
x 266 pix.
= 110.39 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.415 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-2.802024 - 5.280475
Average (Standard dev.)0.0024798277 (±0.35356525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions266266266
Spacing266266266
CellA=B=C: 110.39 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Half map 1 (unmodified)

Fileemd_26916_additional_1.map
AnnotationHalf map 1 (unmodified)
Projections & Slices
AxesZYX

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Additional map: Half map 2 (unmodified)

Fileemd_26916_additional_2.map
AnnotationHalf map 2 (unmodified)
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Additional map: Mask used for FSC calculation.

Fileemd_26916_additional_3.map
AnnotationMask used for FSC calculation.
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AxesZYX

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Additional map: Sharpened original map (B=52.5)

Fileemd_26916_additional_4.map
AnnotationSharpened original map (B=52.5)
Projections & Slices
AxesZYX

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

Fileemd_26916_half_map_1.map
AnnotationHalf map 1 (cropped and resampled).
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_26916_half_map_2.map
AnnotationHalf map 2 (cropped and resampled).
Projections & Slices
AxesZYX

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Sample components

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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: Blood group Rh(CE) polypeptide
    • Protein or peptide: Ammonium transporter Rh type A
    • Protein or peptide: Ankyrin-1
  • Ligand: CHOLESTEROL
  • Ligand: Digitonin
  • Ligand: water

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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-#3
Details: Particle set isolated by 3D classification from mixture mostly containing ankyrin complexes
Source (natural)Organism: Homo sapiens (human) / Organ: Blood / Tissue: Erythrocytes / Location in cell: Plasma membrane

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Macromolecule #1: Blood group Rh(CE) polypeptide

MacromoleculeName: Blood group Rh(CE) polypeptide / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Blood / Tissue: Erythrocytes
Molecular weightTheoretical: 45.598918 KDa
SequenceString: MSSKYPRSVR RCLPLWALTL EAALILLFYF FTHYDASLED QKGLVASYQV GQDLTVMAAL GLGFLTSNFR RHSWSSVAFN LFMLALGVQ WAILLDGFLS QFPPGKVVIT LFSIRLATMS AMSVLISAGA VLGKVNLAQL VVMVLVEVTA LGTLRMVISN I FNTDYHMN ...String:
MSSKYPRSVR RCLPLWALTL EAALILLFYF FTHYDASLED QKGLVASYQV GQDLTVMAAL GLGFLTSNFR RHSWSSVAFN LFMLALGVQ WAILLDGFLS QFPPGKVVIT LFSIRLATMS AMSVLISAGA VLGKVNLAQL VVMVLVEVTA LGTLRMVISN I FNTDYHMN LRHFYVFAAY FGLTVAWCLP KPLPKGTEDN DQRATIPSLS AMLGALFLWM FWPSVNSPLL RSPIQRKNAM FN TYYALAV SVVTAISGSS LAHPQRKISM TYVHSAVLAG GVAVGTSCHL IPSPWLAMVL GLVAGLISIG GAKCLPVCCN RVL GIHHIS VMHSIFSLLG LLGEITYIVL LVLHTVWNGN GMIGFQVLLS IGELSLAIVI ALTSGLLTGL LLNLKIWKAP HVAK YFDDQ VFWKFPHLAV GF

UniProtKB: Blood group Rh(CE) polypeptide

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Macromolecule #2: Ammonium transporter Rh type A

MacromoleculeName: Ammonium transporter Rh type A / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Blood / Tissue: Erythrocytes
Molecular weightTheoretical: 44.229629 KDa
SequenceString: MRFTFPLMAI VLEIAMIVLF GLFVEYETDQ TVLEQLNITK PTDMGIFFEL YPLFQDVHVM IFVGFGFLMT FLKKYGFSSV GINLLVAAL GLQWGTIVQG ILQSQGQKFN IGIKNMINAD FSAATVLISF GAVLGKTSPT QMLIMTILEI VFFAHNEYLV S EIFKASDI ...String:
MRFTFPLMAI VLEIAMIVLF GLFVEYETDQ TVLEQLNITK PTDMGIFFEL YPLFQDVHVM IFVGFGFLMT FLKKYGFSSV GINLLVAAL GLQWGTIVQG ILQSQGQKFN IGIKNMINAD FSAATVLISF GAVLGKTSPT QMLIMTILEI VFFAHNEYLV S EIFKASDI GASMTIHAFG AYFGLAVAGI LYRSGLRKGH ENEESAYYSD LFAMIGTLFL WMFWPSFNSA IAEPGDKQCR AI VNTYFSL AACVLTAFAF SSLVEHRGKL NMVHIQNATL AGGVAVGTCA DMAIHPFGSM IIGSIAGMVS VLGYKFLTPL FTT KLRIHD TCGVHNLHGL PGVVGGLAGI VAVAMGASNT SMAMQAAALG SSIGTAVVGG LMTGLILKLP LWGQPSDQNC YDDS VYWKV PKTR

UniProtKB: Ammonium transporter Rh type A

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Macromolecule #3: Ankyrin-1

MacromoleculeName: Ankyrin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: Blood / Tissue: Erythrocytes
Molecular weightTheoretical: 21.760494 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 PDV

UniProtKB: Ankyrin-1

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #5: Digitonin

MacromoleculeName: Digitonin / type: ligand / ID: 5 / Number of copies: 2 / Formula: AJP
Molecular weightTheoretical: 1.229312 KDa
Chemical component information

ChemComp-AJP:
Digitonin / detergent*YM

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 235 / 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

Startup modelType of model: INSILICO MODEL
In silico model: Generated by stochastic gradient descent using ab intio reconstruction job type in cryoSPARC v3.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 710437
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4yzf


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7uzq:
Local refinement of RhAG-RhCE-ANK1(AR1-5), from consensus refinement of all classes

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