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- PDB-8d9n: CryoEM structures of bAE1 captured in multiple states. -

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Basic information

Entry
Database: PDB / ID: 8d9n
TitleCryoEM structures of bAE1 captured in multiple states.
ComponentsAnion exchange protein
KeywordsTRANSPORT PROTEIN / cryoEM / Band3 / bAE1 (SLC4A1) / anion exchanger / STRUCTURAL PROTEIN
Function / homology
Function and homology information


monoatomic anion transmembrane transporter activity / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity / regulation of intracellular pH / basolateral 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 (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsZhekova, H.R. / Wang, W.G. / Jiang, J.S. / Tsirulnikov, K. / Muhammad-Khan, G.H. / Azimov, R. / Abuladze, N. / Kao, L. / Newman, D. / Noskov, S.Y. ...Zhekova, H.R. / Wang, W.G. / Jiang, J.S. / Tsirulnikov, K. / Muhammad-Khan, G.H. / Azimov, R. / Abuladze, N. / Kao, L. / Newman, D. / Noskov, S.Y. / Tieleman, P. / Zhou, Z.H. / Pushkin, A. / Kurtz, I.
Funding support United States, 2items
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
DepositionJun 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anion exchange protein
B: Anion exchange protein


Theoretical massNumber of molelcules
Total (without water)208,9492
Polymers208,9492
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Anion exchange protein


Mass: 104474.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q9XSW5

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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: band 3 anion transport protein / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.104 MDa / Experimental value: NO
Source (natural)Organism: Bos taurus (cattle)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMTris HydrochlorideTris-HCl1
32 CMCAmphipol-C8PMAL-C81
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: NITROGEN / Humidity: 100 %

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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: OTHER
Electron lensMode: OTHER / Calibrated magnification: 36764 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 52 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 48 / Used frames/image: 1-48

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELION2particle selection
2Leginon3.2image acquisitionLeginon is a system designed for automated collection of images from a transmission electron microscope
4CTFFIND4.1.8CTF correction
7VMD1.9.3model fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIX1.19.2model refinement
CTF correctionDetails: Estimated by CTFFIND4. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2635578
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 251871 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027368
ELECTRON MICROSCOPYf_angle_d0.55210030
ELECTRON MICROSCOPYf_dihedral_angle_d4.325962
ELECTRON MICROSCOPYf_chiral_restr0.041218
ELECTRON MICROSCOPYf_plane_restr0.0051210

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