8T6U

Cryo-EM structure of human Anion Exchanger 1 bound to Dipyridamole

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Substrate binding and inhibition of the anion exchanger 1 transporter.

Capper, M.J., Yang, S., Stone, A.C., Vatansever, S., Zilberg, G., Mathiharan, Y.K., Habib, R., Hutchinson, K., Zhao, Y., Schlessinger, A., Mezei, M., Osman, R., Zhang, B., Wacker, D.

(2023) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-023-01085-6
  • Primary Citation of Related Structures:  
    7TY4, 7TY6, 7TY7, 7TY8, 7TYA, 8T6U, 8T6V

  • PubMed Abstract: 

    • Anion exchanger 1 (AE1), a member of the solute carrier (SLC) family, is the primary bicarbonate transporter in erythrocytes, regulating pH levels and CO 2 transport between lungs and tissues. Previous studies characterized its role in erythrocyte structure and provided insight into transport regulation ...

    Anion exchanger 1 (AE1), a member of the solute carrier (SLC) family, is the primary bicarbonate transporter in erythrocytes, regulating pH levels and CO 2 transport between lungs and tissues. Previous studies characterized its role in erythrocyte structure and provided insight into transport regulation. However, key questions remain regarding substrate binding and transport, mechanisms of drug inhibition and modulation by membrane components. Here we present seven cryo-EM structures in apo, bicarbonate-bound and inhibitor-bound states. These, combined with uptake and computational studies, reveal important molecular features of substrate recognition and transport, and illuminate sterol binding sites, to elucidate distinct inhibitory mechanisms of research chemicals and prescription drugs. We further probe the substrate binding site via structure-based ligand screening, identifying an AE1 inhibitor. Together, our findings provide insight into mechanisms of solute carrier transport and inhibition.

    Organizational Affiliation: 

    Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA. daniel.wacker@mssm.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Band 3 anion transport protein
A, B
523Homo sapiensMutation(s): 0 
Gene Names: SLC4A1, AE1, DI, EPB3
UniProt & NIH Common Fund Data Resources
Find proteins for P02730 (Homo sapiens)
Explore P02730 
Go to UniProtKB:  P02730
PHAROS:  P02730
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02730
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth D],
D [auth L]		2N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1
Download Ideal Coordinates CCD File 
G [auth A],
K [auth A]		1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N		 Ligand Interaction
H9F (Subject of Investigation/LOI)
Query on H9F
Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]		2-[[2-[bis(2-hydroxyethyl)amino]-4,8-di(piperidin-1-yl)pyrimido[5,4-d]pyrimidin-6-yl]-(2-hydroxyethyl)amino]ethanol
C24 H40 N8 O4
IZEKFCXSFNUWAM-UHFFFAOYSA-N		 Ligand Interaction
CLR
Query on CLR
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
I [auth A]
J [auth A]
L [auth B]
E [auth A],
F [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
O [auth B],
P [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMACservalcat
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM133504
Other privateEdward Mallinckrodt, Jr Foundation Grant
Other privateMcKnight Endowment Fund for Neuroscience Scholarship

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Database references, Refinement description