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- PDB-8y86: Human AE3 with NaHCO3- -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8y86
TitleHuman AE3 with NaHCO3-
ComponentsAnion exchange protein 3
KeywordsTRANSPORT PROTEIN / bicarbonate
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 / transmembrane transporter activity ...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 / transmembrane transporter activity / 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
BICARBONATE ION / Anion exchange protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsJian, L. / Zhang, Q. / Yao, D. / Cao, Y.
Funding support China, 2items
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: Jian, L. / Zhang, Q. / Yao, D. / Wang, Q. / Chen, M. / Xia, Y. / Li, S. / Shen, Y. / Cao, M. / Qin, A. / Li, L. / Cao, Y.
History
DepositionFeb 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anion exchange protein 3
B: Anion exchange protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,0454
Polymers271,9232
Non-polymers1222
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Anion exchange protein 3 / AE 3 / Anion exchanger 3


Mass: 135961.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AE3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P48751
#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
Has ligand of interestY

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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 3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.135 MDa / Experimental 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 533919 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038266
ELECTRON MICROSCOPYf_angle_d0.51111254
ELECTRON MICROSCOPYf_dihedral_angle_d3.5511110
ELECTRON MICROSCOPYf_chiral_restr0.0391346
ELECTRON MICROSCOPYf_plane_restr0.0051380

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