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- EMDB-36448: Structure of AE2 in complex with PIP2 -

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Basic information

Entry
Database: EMDB / ID: EMD-36448
TitleStructure of AE2 in complex with PIP2
Map datasharpened map of AE2 in complex with PIP2
Sample
  • Complex: Anion exchange protein 2, isoform A
    • Protein or peptide: Anion exchange protein 2
  • Ligand: CHLORIDE ION
  • Ligand: [(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
KeywordsAE2 / SLC4A2 / PIP2 / membrane protein
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 / digestive tract development / bicarbonate 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 / digestive tract development / bicarbonate transport / monoatomic anion transport / regulation of bone resorption / transmembrane transporter activity / osteoclast differentiation / regulation of actin cytoskeleton organization / regulation of intracellular pH / 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
Anion exchange protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYin YX / Ding D
Funding support China, 2 items
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, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36448.png

Downloads & links

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Map

FileDownload / File: emd_36448.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map of AE2 in complex with PIP2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 328.4 Å		0.82 Å/pix.
x 400 pix.
= 328.4 Å		0.82 Å/pix.
x 400 pix.
= 328.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.821 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.77948254 - 1.2528232
Average (Standard dev.)-0.00006313 (±0.023473114)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A map of AE2 in complex with PIP2

Fileemd_36448_half_map_1.map
Annotationhalf_A map of AE2 in complex with PIP2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B map of AE2 in complex with PIP2

Fileemd_36448_half_map_2.map
Annotationhalf_B map of AE2 in complex with PIP2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Anion exchange protein 2, isoform A

EntireName: Anion exchange protein 2, isoform A
Components
  • Complex: Anion exchange protein 2, isoform A
    • Protein or peptide: Anion exchange protein 2
  • Ligand: CHLORIDE ION
  • Ligand: [(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

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Supramolecule #1: Anion exchange protein 2, isoform A

SupramoleculeName: Anion exchange protein 2, isoform A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Anion exchange protein 2

MacromoleculeName: Anion exchange protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 137.176906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSAPRRPAK GADSFCTPEP ESLGPGTPGF PEQEEDELHR TLGVERFEEI LQEAGSRGGE EPGRSYGEED FEYHRQSSHH IHHPLSTHL PPDARRRKTP QGPGRKPRRR PGASPTGETP TIEEGEEDED EASEAEGARA LTQPSPVSTP SSVQFFLQED D SADRKAER ...String:
MSSAPRRPAK GADSFCTPEP ESLGPGTPGF PEQEEDELHR TLGVERFEEI LQEAGSRGGE EPGRSYGEED FEYHRQSSHH IHHPLSTHL PPDARRRKTP QGPGRKPRRR PGASPTGETP TIEEGEEDED EASEAEGARA LTQPSPVSTP SSVQFFLQED D SADRKAER TSPSSPAPLP HQEATPRASK GAQAGTQVEE AEAEAVAVAS GTAGGDDGGA SGRPLPKAQP GHRSYNLQER RR IGSMTGA EQALLPRVPT DEIEAQTLAT ADLDLMKSHR FEDVPGVRRH LVRKNAKGST QSGREGREPG PTPRARPRAP HKP HEVFVE LNELLLDKNQ EPQWRETARW IKFEEDVEEE TERWGKPHVA SLSFRSLLEL RRTLAHGAVL LDLDQQTLPG VAHQ VVEQM VISDQIKAED RANVLRALLL KHSHPSDEKD FSFPRNISAG SLGSLLGHHH GQGAESDPHV TEPLMGGVPE TRLEV ERER ELPPPAPPAG ITRSKSKHEL KLLEKIPENA EATVVLVGCV EFLSRPTMAF VRLREAVELD AVLEVPVPVR FLFLLL GPS SANMDYHEIG RSISTLMSDK QFHEAAYLAD EREDLLTAIN AFLDCSVVLP PSEVQGEELL RSVAHFQRQM LKKREEQ GR LLPTGAGLEP KSAQDKALLQ MVEAAGAAED DPLRRTGRPF GGLIRDVRRR YPHYLSDFRD ALDPQCLAAV IFIYFAAL S PAITFGGLLG EKTQDLIGVS ELIMSTALQG VVFCLLGAQP LLVIGFSGPL LVFEEAFFSF CSSNHLEYLV GRVWIGFWL VFLALLMVAL EGSFLVRFVS RFTQEIFAFL ISLIFIYETF YKLVKIFQEH PLHGCSASNS SEVDGGENMT WAGARPTLGP GNRSLAGQS GQGKPRGQPN TALLSLVLMA GTFFIAFFLR KFKNSRFFPG RIRRVIGDFG VPIAILIMVL VDYSIEDTYT Q KLSVPSGF SVTAPEKRGW VINPLGEKSP FPVWMMVASL LPAILVFILI FMETQITTLI ISKKERMLQK GSGFHLDLLL IV AMGGICA LFGLPWLAAA TVRSVTHANA LTVMSKAVAP GDKPKIQEVK EQRVTGLLVA LLVGLSIVIG DLLRQIPLAV LFG IFLYMG VTSLNGIQFY ERLHLLLMPP KHHPDVTYVK KVRTLRMHLF TALQLLCLAL LWAVMSTAAS LAFPFILILT VPLR MVVLT RIFTDREMKC LDANEAEPVF DEREGVDEYN EMPMPV

UniProtKB: Anion exchange protein 2

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Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #3: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tr...

MacromoleculeName: [(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
type: ligand / ID: 3 / Number of copies: 2 / Formula: PT5
Molecular weightTheoretical: 1.047088 KDa

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.0) / Number images used: 107451
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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