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- PDB-8jni: Structure of AE2 in complex with PIP2 -

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Basic information

Entry
Database: PDB / ID: 8jni
TitleStructure of AE2 in complex with PIP2
ComponentsAnion exchange protein 2
KeywordsMEMBRANE PROTEIN / AE2 / SLC4A2 / PIP2
Function / homology
Function and homology information


negative regulation of CD8-positive, alpha-beta T cell differentiation / negative regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of enamel mineralization / Bicarbonate transporters / amelogenesis / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transport / monoatomic anion transport ...negative regulation of CD8-positive, alpha-beta T cell differentiation / negative regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of enamel mineralization / Bicarbonate transporters / amelogenesis / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transport / monoatomic anion transport / digestive tract development / regulation of bone resorption / osteoclast differentiation / regulation of intracellular pH / regulation of actin cytoskeleton organization / transmembrane transport / spermatogenesis / basolateral plasma membrane / apical plasma membrane / focal adhesion / enzyme binding / membrane / plasma membrane
Similarity search - Function
Anion exchange protein 2 / 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
Chem-PT5 / Anion exchange protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYin, Y.X. / Ding, D.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81874235 China
National Natural Science Foundation of China (NSFC)82030081 China
CitationJournal: Nat Commun / Year: 2024
Title: Structural and functional insights into the lipid regulation of human anion exchanger 2.
Authors: Weiqi Zhang / Dian Ding / Yishuo Lu / Hongyi Chen / Peijun Jiang / Peng Zuo / Guangxi Wang / Juan Luo / Yue Yin / Jianyuan Luo / Yuxin Yin /
Abstract: Anion exchanger 2 (AE2) is an electroneutral Na-independent Cl/HCO exchanger belongs to the SLC4 transporter family. The widely expressed AE2 participates in a variety of physiological processes, ...Anion exchanger 2 (AE2) is an electroneutral Na-independent Cl/HCO exchanger belongs to the SLC4 transporter family. The widely expressed AE2 participates in a variety of physiological processes, including transepithelial acid-base secretion and osteoclastogenesis. Both the transmembrane domains (TMDs) and the N-terminal cytoplasmic domain (NTD) are involved in regulation of AE2 activity. However, the regulatory mechanism remains unclear. Here, we report a 3.2 Å cryo-EM structure of the AE2 TMDs in complex with PIP and a 3.3 Å full-length mutant AE2 structure in the resting state without PIP. We demonstrate that PIP at the TMD dimer interface is involved in the substrate exchange process. Mutation in the PIP binding site leads to the displacement of TM7 and further stabilizes the interaction between the TMD and the NTD. Reduced substrate transport activity and conformation similar to AE2 in acidic pH indicating the central contribution of PIP to the function of AE2.
History
DepositionJun 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Anion exchange protein 2
A: Anion exchange protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,5196
Polymers274,3542
Non-polymers2,1654
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Anion exchange protein 2 / AE 2 / Anion exchanger 2 / Non-erythroid band 3-like protein / BND3L / Solute carrier family 4 member 2


Mass: 137176.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC4A2, AE2, EPB3L1, HKB3, MPB3L / Production host: Homo sapiens (human) / References: UniProt: P04920
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PT5 / [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate / Phosphatidylinositol 4,5-bisphosphate / PtdIns(4,5)P2


Mass: 1047.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H85O19P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationY

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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: Anion exchange protein 2, isoform A / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 52 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: cryoSPARC / Version: 3.1.0 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107451 / Symmetry type: POINT

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