6CAA

CryoEM structure of human SLC4A4 sodium-coupled acid-base transporter NBCe1

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens

  • Deposited: 2018-01-29 Released: 2018-03-07 
  • Deposition Author(s): Huynh, K.W., Jiang, J., Abuladze, N., Tsirulnikov, K., Kao, L., Shao, X., Newman, D., Azimov, R., Pushkin, A., Zhou, Z.H., Kurtz, I.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease; Allan Smidt Charitable Fund; Factor Family Foundation; Ralph Block Family Foundation; National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Institute of Dental and Craniofacial Research; National Institutes of Health/National Institute Of Allergy and Infectious Diseases; National Institutes of Health/National Center for Research Resources; National Science Foundation (United States) 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

CryoEM structure of the human SLC4A4 sodium-coupled acid-base transporter NBCe1.

Huynh, K.W.Jiang, J.Abuladze, N.Tsirulnikov, K.Kao, L.Shao, X.Newman, D.Azimov, R.Pushkin, A.Zhou, Z.H.Kurtz, I.

(2018) Nat Commun 9: 900-900

  • DOI: 10.1038/s41467-018-03271-3

  • PubMed Abstract: 
  • Na <sup>+ </sup>-coupled acid-base transporters play essential roles in human biology. Their dysfunction has been linked to cancer, heart, and brain disease. High-resolution structures of mammalian Na <sup>+ </sup>-coupled acid-base transporters are ...

    Na + -coupled acid-base transporters play essential roles in human biology. Their dysfunction has been linked to cancer, heart, and brain disease. High-resolution structures of mammalian Na + -coupled acid-base transporters are not available. The sodium-bicarbonate cotransporter NBCe1 functions in multiple organs and its mutations cause blindness, abnormal growth and blood chemistry, migraines, and impaired cognitive function. Here, we have determined the structure of the membrane domain dimer of human NBCe1 at 3.9 Å resolution by cryo electron microscopy. Our atomic model and functional mutagenesis revealed the ion accessibility pathway and the ion coordination site, the latter containing residues involved in human disease-causing mutations. We identified a small number of residues within the ion coordination site whose modification transformed NBCe1 into an anion exchanger. Our data suggest that symporters and exchangers utilize comparable transport machinery and that subtle differences in their substrate-binding regions have very significant effects on their transport mode.


    Organizational Affiliation

    California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Neurobiology, University of California, Los Angeles, CA, 90095, USA.,Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, 90095, USA.,Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. apushkin@mednet.ucla.edu.,Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, 90095, USA. Hong.Zhou@ucla.edu.,Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. ikurtz@mednet.ucla.edu.,Brain Research Institute, University of California, Los Angeles, CA, 90095, USA. ikurtz@mednet.ucla.edu.,Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.,California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA. Hong.Zhou@ucla.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Electrogenic sodium bicarbonate cotransporter 1
A, B
1035Homo sapiensMutation(s): 0 
Gene Names: SLC4A4 (NBC, NBC1, NBCE1)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Solute Carrier (SLC) Transporter Superfamily
Protein: 
SLC4A4 Na+-coupled acid-base transporter NBCe1
Find proteins for Q9Y6R1 (Homo sapiens)
Go to Gene View: SLC4A4
Go to UniProtKB:  Q9Y6R1
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK077162
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK007789
Allan Smidt Charitable FundUnited States--
Factor Family FoundationUnited States--
Ralph Block Family FoundationUnited States--
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM071940
National Institutes of Health/National Institute of Dental and Craniofacial ResearchUnited StatesDE025567
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI094386
National Institutes of Health/National Center for Research ResourcesUnited States1S10RR23057
National Institutes of Health/National Institute of General Medical SciencesUnited States1U24GM116792
National Science Foundation (United States)United StatesDBI-1338135

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-14
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Data collection
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection