2W2E

1.15 Angstrom crystal structure of P.pastoris aquaporin, Aqy1, in a closed conformation at pH 3.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.165 
  • R-Value Observed: 0.140 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of a Yeast Aquaporin at 1.15 A Reveals a Novel Gating Mechanism.1.15 A

Fischer, G.Kosinska-Eriksson, U.Aponte-Santamaria, C.Palmgren, M.Geijer, C.Hedfalk, K.Hohmann, S.De Groot, B.L.Neutze, R.Lindkvist-Petersson, K.

(2009) PLoS Biol 7: E130

  • DOI: https://doi.org/10.1371/journal.pbio.1000130
  • Primary Citation of Related Structures:  
    2W1P, 2W2E

  • PubMed Abstract: 

    Aquaporins are transmembrane proteins that facilitate the flow of water through cellular membranes. An unusual characteristic of yeast aquaporins is that they frequently contain an extended N terminus of unknown function. Here we present the X-ray structure of the yeast aquaporin Aqy1 from Pichia pastoris at 1.15 A resolution. Our crystal structure reveals that the water channel is closed by the N terminus, which arranges as a tightly wound helical bundle, with Tyr31 forming H-bond interactions to a water molecule within the pore and thereby occluding the channel entrance. Nevertheless, functional assays show that Aqy1 has appreciable water transport activity that aids survival during rapid freezing of P. pastoris. These findings establish that Aqy1 is a gated water channel. Mutational studies in combination with molecular dynamics simulations imply that gating may be regulated by a combination of phosphorylation and mechanosensitivity.


  • Organizational Affiliation

    Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, Göteborg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AQUAPORIN PIP2-7 7279Komagataella pastorisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for F2QVG4 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore F2QVG4 
Go to UniProtKB:  F2QVG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2QVG4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.165 
  • R-Value Observed: 0.140 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.447α = 90
b = 91.447β = 90
c = 80.819γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2012-04-11
    Changes: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2019-05-22
    Changes: Advisory, Data collection, Other, Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2023-12-13
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary