5JHO | pdb_00005jho

Crystal structure of the regulatory domain of the sodium driven chloride bicarbonate exchanger.

• PDB DOI: https://doi.org/10.2210/pdb5JHO/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-21 Released: 2017-08-16 
• Deposition Author(s): Alvadia, C., Sommer, T., Bjerregaard-Andersen, K., Morth, J.P.
• Funding Organization(s): Research Council of Norway, Lundbeck foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.238 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

The crystal structure of the regulatory domain of the human sodium-driven chloride/bicarbonate exchanger.

Alvadia, C.M., Sommer, T., Bjerregaard-Andersen, K., Damkier, H.H., Montrasio, M., Aalkjaer, C., Morth, J.P.

(2017) Sci Rep 7: 12131-12131

• PubMed: 28935959 
• DOI: https://doi.org/10.1038/s41598-017-12409-0
• Primary Citation Related Structures: 
  5JHO


• PubMed Abstract: 
  

  The sodium-driven chloride/bicarbonate exchanger (NDCBE) is essential for maintaining homeostatic pH in neurons. The crystal structure at 2.8 Å resolution of the regulatory N-terminal domain of human NDCBE represents the first crystal structure of an electroneutral sodium-bicarbonate cotransporter. The crystal structure forms an equivalent dimeric interface as observed for the cytoplasmic domain of Band 3, and thus establishes that the consensus motif VTVLP is the key minimal dimerization motif. The VTVLP motif is highly conserved and likely to be the physiologically relevant interface for all other members of the SLC4 family. A novel conserved Zn ²⁺ -binding motif present in the N-terminal domain of NDCBE is identified and characterized in vitro. Cellular studies confirm the Zn ²⁺ dependent transport of two electroneutral bicarbonate transporters, NCBE and NBCn1. The Zn ²⁺ site is mapped to a cluster of histidines close to the conserved ETARWLKFEE motif and likely plays a role in the regulation of this important motif. The combined structural and bioinformatics analysis provides a model that predicts with additional confidence the physiologically relevant interface between the cytoplasmic domain and the transmembrane domain.

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Organizational Affiliation: 
• Norwegian Centre for Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349, Oslo, Norway.
Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark.
Norwegian Centre for Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349, Oslo, Norway. [e-mail].
Institute for Experimental Medical Research, Oslo University Hospital, N-0424, Oslo, Norway. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.81 kDa 
• Atom Count: 3,784 
• Modeled Residue Count: 473 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Electroneutral sodium bicarbonate exchanger 1	A, B	344	Homo sapiens	Mutation(s): 0  Gene Names: SLC4A8, KIAA0739, NBC, NBC3, NDCBE1
UniProt & NIH Common Fund Data Resources
Find proteins for Q2Y0W8 (Homo sapiens) Explore Q2Y0W8  Go to UniProtKB:  Q2Y0W8
PHAROS:  Q2Y0W8 GTEx:  ENSG00000050438

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.238 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.04	α = 90
b = 98.04	β = 90
c = 212.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Alvadia, C., Sommer, T., Bjerregaard-Andersen, K., Morth, J.P.

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Funding Organization	Location	Grant Number
Research Council of Norway	Norway	ES486454
Lundbeck foundation	Denmark	R34-A3616

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Database references
• Version 1.2: 2018-01-31
  Changes: Author supporting evidence
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references