4IA4 | pdb_00004ia4

Structure of the spinach aquaporin SoPIP2;1 at pH 6

• PDB DOI: https://doi.org/10.2210/pdb4IA4/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Spinacia oleracea
• Expression System: Komagataella pastoris
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2012-12-06 Released: 2013-05-29 
• Deposition Author(s): Frick, A., Jarva, M., Tornroth-Horsefield, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.243 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Structural basis for pH gating of plant aquaporins

Frick, A., Jarva, M., Tornroth-Horsefield, S.

(2013) FEBS Lett 587: 989-993

• PubMed: 23454640 
• DOI: https://doi.org/10.1016/j.febslet.2013.02.038
• Primary Citation Related Structures: 
  4IA4


• PubMed Abstract: 
  

  Plants have evolved to cope with fluctuations in water supply by gating their water channels known as aquaporins. During flooding, a rapid drop of cytosolic pH due to anoxia leads to a simultaneous closure of the aquaporins in the plasma membrane. The closing mechanism has been suggested to involve a conserved histidine on cytosolic loop D. Here we report the crystal structure of a spinach aquaporin at low pH, revealing for the first time the structural basis for how this pH-sensitive histidine helps to keep the aquaporin in a closed state.

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Organizational Affiliation: 
• Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 122.13 kDa 
• Atom Count: 7,290 
• Modeled Residue Count: 967 
• Deposited Residue Count: 1,124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aquaporin	A, B, C, D	281	Spinacia oleracea	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q41372 (Spinacia oleracea) Explore Q41372  Go to UniProtKB:  Q41372

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.243 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.227	α = 90
b = 104.19	β = 90
c = 66.523	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): Frick, A., Jarva, M., Tornroth-Horsefield, S.

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary