4YZF

Crystal structure of the anion exchanger domain of human erythrocyte Band 3

• PDB DOI:  https://doi.org/10.2210/pdb4YZF/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2015-03-25 Released: 2015-11-04 
• Deposition Author(s): Alguel, Y., Arakawa, T., Yugiri, T.K., Iwanari, H., Hatae, H., Iwata, M., Abe, Y., Hino, T., Suno, C.I., Kuma, H., Kang, D., Murata, T., Hamakubo, T., Cameron, A.D., Kobayashi, T., Hamasaki, N., Iwata, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.290 
• R-Value Work: 0.274 
• R-Value Observed: 0.275 

Literature

Crystal structure of the anion exchanger domain of human erythrocyte band 3.

Arakawa, T., Kobayashi-Yurugi, T., Alguel, Y., Iwanari, H., Hatae, H., Iwata, M., Abe, Y., Hino, T., Ikeda-Suno, C., Kuma, H., Kang, D., Murata, T., Hamakubo, T., Cameron, A.D., Kobayashi, T., Hamasaki, N., Iwata, S.

(2015) Science 350: 680-684

• PubMed: 26542571 
• DOI: https://doi.org/10.1126/science.aaa4335
• Primary Citation of Related Structures:  
  4YZF, 5A16


• PubMed Abstract: 
  

Anion exchanger 1 (AE1), also known as band 3 or SLC4A1, plays a key role in the removal of carbon dioxide from tissues by facilitating the exchange of chloride and bicarbonate across the plasma membrane of erythrocytes. An isoform of AE1 is also present in the kidney. Specific mutations in human AE1 cause several types of hereditary hemolytic anemias and/or distal renal tubular acidosis. Here we report the crystal structure of the band 3 anion exchanger domain (AE1(CTD)) at 3.5 angstroms. The structure is locked in an outward-facing open conformation by an inhibitor. Comparing this structure with a substrate-bound structure of the uracil transporter UraA in an inward-facing conformation allowed us to identify the anion-binding position in the AE1(CTD), and to propose a possible transport mechanism that could explain why selected mutations lead to disease.

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Organizational Affiliation: 

Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO) Human Receptor Crystallography Project, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan. JST, Research Acceleration Program, Membrane Protein Crystallography Project, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan. Department of Cell Biology, Kyoto University Faculty of Medicine, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan. Division of Molecular Biosciences, Membrane Protein Crystallography group, Imperial College London, London SW7 2AZ, UK. Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 0DE, UK. Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire OX11 0FA, UK. Platform for Drug Discovery, Informatics, and Structural Life Science, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 601.72 kDa 
• Atom Count: 28,724 
• Modelled Residue Count: 3,664 
• Deposited Residue Count: 5,408 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Band 3 anion transport protein	A, B, C, D	911	Homo sapiens	Mutation(s): 0  Gene Names: SLC4A1, AE1, DI, EPB3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P02730 (Homo sapiens) Explore P02730  Go to UniProtKB:  P02730
PHAROS:  P02730

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB fragment of Immunoglobulin (IgG) molecule	E, G, I, K	223	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB fragment of Immunoglobulin (IgG) molecule	F, H, J, L	218	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4KU	M [auth A], N [auth B], O [auth C], P [auth D]	2,2'-ethane-1,2-diylbis{5-[(sulfanylmethyl)amino]benzenesulfonic acid} C16 H20 N2 O6 S4 LJEHNCSYWIAXRX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.290 
• R-Value Work: 0.274 
• R-Value Observed: 0.275 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.825	α = 90
b = 171.957	β = 101.16
c = 271.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
SHARP	phasing
Coot	model building
O	model building
xia2	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-04 
Deposition Author(s): Alguel, Y., Arakawa, T., Yugiri, T.K., Iwanari, H., Hatae, H., Iwata, M., Abe, Y., Hino, T., Suno, C.I., Kuma, H., Kang, D., Murata, T., Hamakubo, T., Cameron, A.D., Kobayashi, T., Hamasaki, N., Iwata, S.

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 1.1: 2015-11-18
  Changes: Database references