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- EMDB-28055: CryoEM structures of bAE1 captured in multiple states. -

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Basic information

Entry
Database: EMDB / ID: EMD-28055
TitleCryoEM structures of bAE1 captured in multiple states.
Map dataFull map.
Sample
  • Organelle or cellular component: Full-length bovine band 3 anion transport protein.
    • Protein or peptide: Anion exchange protein
KeywordscryoEM / Band3 / bAE1 (SLC4A1) / anion exchanger / STRUCTURAL PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


monoatomic anion transmembrane transporter activity / solute:inorganic anion antiporter activity / plasma membrane
Similarity search - Function
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 / Phosphotransferase/anion transporter / Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter integral membrane domain
Similarity search - Domain/homology
Anion exchange protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsZhekova HR / Wang WG / Jiang JS / Tsirulnikov K / Muhammad-Khan GH / Azimov R / Abuladze N / Kao L / Newman D / Noskov SY ...Zhekova HR / Wang WG / Jiang JS / Tsirulnikov K / Muhammad-Khan GH / Azimov R / Abuladze N / Kao L / Newman D / Noskov SY / Tieleman P / Zhou ZH / Pushkin A / Kurtz I
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK077162 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01GM071940 United States
CitationJournal: Commun Biol / Year: 2022
Title: CryoEM structures of anion exchanger 1 capture multiple states of inward- and outward-facing conformations.
Authors: Hristina R Zhekova / Jiansen Jiang / Weiguang Wang / Kirill Tsirulnikov / Gülru Kayık / Hanif Muhammad Khan / Rustam Azimov / Natalia Abuladze / Liyo Kao / Debbie Newman / Sergei Yu Noskov ...Authors: Hristina R Zhekova / Jiansen Jiang / Weiguang Wang / Kirill Tsirulnikov / Gülru Kayık / Hanif Muhammad Khan / Rustam Azimov / Natalia Abuladze / Liyo Kao / Debbie Newman / Sergei Yu Noskov / D Peter Tieleman / Z Hong Zhou / Alexander Pushkin / Ira Kurtz /
Abstract: Anion exchanger 1 (AE1, band 3) is a major membrane protein of red blood cells and plays a key role in acid-base homeostasis, urine acidification, red blood cell shape regulation, and removal of ...Anion exchanger 1 (AE1, band 3) is a major membrane protein of red blood cells and plays a key role in acid-base homeostasis, urine acidification, red blood cell shape regulation, and removal of carbon dioxide during respiration. Though structures of the transmembrane domain (TMD) of three SLC4 transporters, including AE1, have been resolved previously in their outward-facing (OF) state, no mammalian SLC4 structure has been reported in the inward-facing (IF) conformation. Here we present the cryoEM structures of full-length bovine AE1 with its TMD captured in both IF and OF conformations. Remarkably, both IF-IF homodimers and IF-OF heterodimers were detected. The IF structures feature downward movement in the core domain with significant unexpected elongation of TM11. Molecular modeling and structure guided mutagenesis confirmed the functional significance of residues involved in TM11 elongation. Our data provide direct evidence for an elevator-like mechanism of ion transport by an SLC4 family member.
History
DepositionSep 7, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28055.png

Downloads & links

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Map

FileDownload / File: emd_28055.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 192 pix.
= 261.12 Å		1.36 Å/pix.
x 192 pix.
= 261.12 Å		1.36 Å/pix.
x 192 pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0496
Minimum - Maximum-0.030246677 - 0.13289298
Average (Standard dev.)0.000023135892 (±0.0076170256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half1.

Fileemd_28055_half_map_1.map
AnnotationHalf1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half2

Fileemd_28055_half_map_2.map
AnnotationHalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full-length bovine band 3 anion transport protein.

EntireName: Full-length bovine band 3 anion transport protein.
Components
  • Organelle or cellular component: Full-length bovine band 3 anion transport protein.
    • Protein or peptide: Anion exchange protein

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Supramolecule #1: Full-length bovine band 3 anion transport protein.

SupramoleculeName: Full-length bovine band 3 anion transport protein. / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 104 KDa

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Macromolecule #1: Anion exchange protein

MacromoleculeName: Anion exchange protein / type: protein_or_peptide / ID: 1
Details: Chain A and C are the TMD of bovine AE1. Chain B and D are the cytoplasmic domain of bovine AE1. Some loops are missing because of insufficient resolution.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 104.474258 KDa
SequenceString: MGDPEEYEDQ LEETLEQKEY EDHDSVSIPM EEAEGDTIQE EEAEARVNQL TDTDYHTTSQ HPETHKVCVQ LRELVMDEKN QEIQWMETA RWVGLEENLG KDGIWGRPHL PYLNFWSLLE LQKAFAKGTV LLDLPGKSLA EVANQLLDRF TFEGQIQPDD Q DNLLRVLL ...String:
MGDPEEYEDQ LEETLEQKEY EDHDSVSIPM EEAEGDTIQE EEAEARVNQL TDTDYHTTSQ HPETHKVCVQ LRELVMDEKN QEIQWMETA RWVGLEENLG KDGIWGRPHL PYLNFWSLLE LQKAFAKGTV LLDLPGKSLA EVANQLLDRF TFEGQIQPDD Q DNLLRVLL LKHSHASDME ALGGVKPVVV THSGDPSEPL LPQHPSLETE LFCEQGEGST RGHAPEILGK SPQDWEATLV LV GCARFLK RPVLGFVRLK EPMEPEPKPE GSEEPAVPVR FLIVLLGPEG PNINYTQLGR AAATLMSERV FWNDAYLAQS KET LVQSLE GFLDCSLVLP PLDAPSEKAL LSLVPVQKEL LRRRYLPSPA KPDPSIFKDL DVKKGPGDTP EDPLQRTGKL FGGL VRDIR RRYPRYLSDI TDALSPQVLS AIIFIYFAAL TPAITFGGLL GDKTENMIGV SELLLSTALQ GIIFSLLGAQ PLLVL GFSG PLLVFEEAFY SFCQTNNLEY IVGRVWIGFW LILLVVLVVA FEGSFLVRFI SRYTQEIFSF LISLIFIYET FYKLVT IFQ DHPLQKNYDH DVLTTPKPQA ALPNTALLSL VLMAGTFFLA MMLRKFKNSS YFPGKLRRII GDFGVPISIL IMVMVDA LI QDTYTQKLSV PEGLSVSNPT ERDWLIHPLG IRVEFPIWMM FASALPALLV FILIFLESQI TTLIISKPER KMVKGSGF H LDLLLIIGMG GVGAIFGMPW LSATTVRTVT HANALTVMSK DSTPGAVSQI QGVKEQRISG LLVAVLVGVS ILMGPVLRH IPLAVLFGIF LYMGVTSLSG IQLFDRVLLL LKPRKYYPEV PYARRVKTWR MHLFTITQIV CLVVLWVVRS IKQISLALPF ILILTVPLR RFLLPFIFRD MELKLLDADD VKLNLDEQNG QDEYDEVAMP V

UniProtKB: Anion exchange protein

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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

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMTris-HClTris Hydrochloride
2.0 CMCPMAL-C8Amphipol-C8
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-48 / Average exposure time: 12.0 sec. / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 36764 / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.4000000000000001 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

Particle selectionNumber selected: 2635578
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4yzf

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 90818
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8eeq:
CryoEM structures of bAE1 captured in multiple states.

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