3I5D

Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.5 Angstroms (R3)

• PDB DOI: https://doi.org/10.2210/pdb3I5D/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Danio rerio
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2009-07-05 Released: 2009-08-04 
• Deposition Author(s): Kawate, T., Michel, J.C., Gouaux, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.46 Å
• R-Value Free: 0.289 
• R-Value Work: 0.276 
• R-Value Observed: 0.277 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 123.65 kDa 
• Atom Count: 7,297 
• Modelled Residue Count: 977 
• Deposited Residue Count: 1,068 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P2X purinoceptor	A, B, C	356	Danio rerio	Mutation(s): 1  Gene Names: p2rx4a, P2X4.1 Membrane Entity: Yes
UniProt
Find proteins for Q6NYR1 (Danio rerio) Explore Q6NYR1  Go to UniProtKB:  Q6NYR1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	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 C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.46 Å
• R-Value Free: 0.289 
• R-Value Work: 0.276 
• R-Value Observed: 0.277 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 234.91	α = 90
b = 234.91	β = 90
c = 138.433	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Kawate, T., Michel, J.C., Gouaux, E.

Revision History  

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-10-13
  Changes: Database references, Structure summary