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- EMDB-39035: Human AE3 with NaHCO3- -

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Basic information

Entry
Database: EMDB / ID: EMD-39035
TitleHuman AE3 with NaHCO3-
Map data
Sample
  • Complex: Anion exchange protein 3
    • Protein or peptide: Anion exchange protein 3
  • Ligand: BICARBONATE ION
Keywordsbicarbonate / TRANSPORT PROTEIN
Function / homology
Function and homology information


pH reduction / cardiac muscle cell action potential / Bicarbonate transporters / cardiac conduction / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / regulation of cardiac muscle cell action potential / transport across blood-brain barrier ...pH reduction / cardiac muscle cell action potential / Bicarbonate transporters / cardiac conduction / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / regulation of cardiac muscle cell action potential / transport across blood-brain barrier / regulation of intracellular pH / transmembrane transport / external side of plasma membrane / membrane / plasma membrane
Similarity search - Function
Anion exchange protein 3 / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsJian L / Zhang Q / Yao D / Cao Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82272519 China
National Natural Science Foundation of China (NSFC)82072468 China
CitationJournal: Nat Commun / Year: 2024
Title: The structural insight into the functional modulation of human anion exchanger 3.
Authors: Liyan Jian / Qing Zhang / Deqiang Yao / Qian Wang / Moxin Chen / Ying Xia / Shaobai Li / Yafeng Shen / Mi Cao / An Qin / Lin Li / Yu Cao /
Abstract: Anion exchanger 3 (AE3) is pivotal in regulating intracellular pH across excitable tissues, yet its structural intricacies and functional dynamics remain underexplored compared to other anion ...Anion exchanger 3 (AE3) is pivotal in regulating intracellular pH across excitable tissues, yet its structural intricacies and functional dynamics remain underexplored compared to other anion exchangers. This study unveils the structural insights into human AE3, including the cryo-electron microscopy structures for AE3 transmembrane domains (TMD) and a chimera combining AE3 N-terminal domain (NTD) with AE2 TMD (hAE32). Our analyzes reveal a substrate binding site, an NTD-TMD interlock mechanism, and a preference for an outward-facing conformation. Unlike AE2, which has more robust acid-loading capabilities, AE3's structure, including a less stable inward-facing conformation due to missing key NTD-TMD interactions, contributes to its moderated pH-modulating activity and increased sensitivity to the inhibitor DIDS. These structural differences underline AE3's distinct functional roles in specific tissues and underscore the complex interplay between structural dynamics and functional specificity within the anion exchanger family, enhancing our understanding of the physiological and pathological roles of the anion exchanger family.
History
DepositionFeb 6, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39035.png

Downloads & links

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Map

FileDownload / File: emd_39035.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-3.9892263 - 7.1502085
Average (Standard dev.)0.0009579429 (±0.13761812)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39035_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39035_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Anion exchange protein 3

EntireName: Anion exchange protein 3
Components
  • Complex: Anion exchange protein 3
    • Protein or peptide: Anion exchange protein 3
  • Ligand: BICARBONATE ION

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Supramolecule #1: Anion exchange protein 3

SupramoleculeName: Anion exchange protein 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135 KDa

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Macromolecule #1: Anion exchange protein 3

MacromoleculeName: Anion exchange protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135.961516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MANGVIPPPG GASPLPQVRV PLEEPPLSPD VEEEDDDLGK TLAVSRFGDL ISKPPAWDPE KPSRSYSERD FEFHRHTSHH THHPLSARL PPPHKLRRLP PTSARHTRRK RKKEKTSAPP SEGTPPIQEE GGAGVDEEEE EEEEEEGESE AEPVEPPHSG T PQKAKFSI ...String:
MANGVIPPPG GASPLPQVRV PLEEPPLSPD VEEEDDDLGK TLAVSRFGDL ISKPPAWDPE KPSRSYSERD FEFHRHTSHH THHPLSARL PPPHKLRRLP PTSARHTRRK RKKEKTSAPP SEGTPPIQEE GGAGVDEEEE EEEEEEGESE AEPVEPPHSG T PQKAKFSI GSDEDDSPGL PGRAAVTKPL PSVGPHTDKS PQHSSSSPSP RARASRLAGE KSRPWSPSAS YDLRERLCPG SA LGNPGGP EQQVPTDEAE AQMLGSADLD DMKSHRLEDN PGVRRHLVKK PSRTQGGRGS PSGLAPILRR KKKKKKLDRR PHE VFVELN ELMLDRSQEP HWRETARWIK FEEDVEEETE RWGKPHVASL SFRSLLELRR TIAHGAALLD LEQTTLPGIA HLVV ETMIV SDQIRPEDRA SVLRTLLLKH SHPNDDKDSG FFPRNPSSSS MNSVLGNHHP TPSHGPDGAV PTMADDLGEP APLWP HDPD AKEKPLHMPG GDGHRGKSLK LLEKIPEDAE ATVVLVGCVP FLEQPAAAFV RLNEAVLLES VLEVPVPVRF LFVMLG PSH TSTDYHELGR SIATLMSDKL FHEAAYQADD RQDLLSAISE FLDGSIVIPP SEVEGRDLLR SVAAFQRELL RKRRERE QT KVEMTTRGGY TAPGKELSLE LGGSEATPED DPLLRTGSVF GGLVRDVRRR YPHYPSDLRD ALHSQCVAAV LFIYFAAL S PAITFGGLLG EKTEGLMGVS ELIVSTAVLG VLFSLLGAQP LLVVGFSGPL LVFEEAFFKF CRAQDLEYLT GRVWVGLWL VVFVLALVAA EGSFLVRYIS PFTQEIFAFL ISLIFIYETF YKLYKVFTEH PLLPFYPPEG ALEGSLDAGL EPNGSALPPT EGPPSPRNQ PNTALLSLIL MLGTFFIAFF LRKFRNSRFL GGKARRIIGD FGIPISILVM VLVDYSITDT YTQKLTVPTG L SVTSPDKR SWFIPPLGSA RPFPPWMMVA AAVPALLVLI LIFMETQITA LIVSQKARRL LKGSGFHLDL LLIGSLGGLC GL FGLPWLT AATVRSVTHV NALTVMRTAI APGDKPQIQE VREQRVTGVL IASLVGLSIV MGAVLRRIPL AVLFGIFLYM GVT SLSGIQ LSQRLLLILM PAKHHPEQPY VTKVKTWRMH LFTCIQLGCI ALLWVVKSTA ASLAFPFLLL LTVPLRHCLL PRLF QDREL QALDSEDAEP NFDEDGQDEY NELHMPV

UniProtKB: Anion exchange protein 3

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Macromolecule #2: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

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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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 533919
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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