3H9V

Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.1 Angstroms

PDB DOI: https://doi.org/10.2210/pdb3H9V/pdb

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

Deposited: 2009-04-30 Released: 2009-07-28
Deposition Author(s): Kawate, T., Michel, J.C., Gouaux, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.278
R-Value Work: 0.248
R-Value Observed: 0.249

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 41.46 kDa
Atom Count: 2,501
Modelled Residue Count: 329
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P2X purinoceptor	A	356	Danio rerio	Mutation(s): 4 Gene Names: p2rx4a, P2X4.1 Membrane Entity: Yes
UniProt
Find proteins for Q6NYR1 (Danio rerio) Explore Q6NYR1 Go to UniProtKB: Q6NYR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NYR1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	B, C	2		N-Glycosylation	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GD Query on GD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	GADOLINIUM ATOM Gd UIWYJDYFSGRHKR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.278
R-Value Work: 0.248
R-Value Observed: 0.249
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.836	α = 90
b = 100.836	β = 90
c = 431.316	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-07-28

Deposition Author(s):

Kawate, T.

Michel, J.C.

Gouaux, E.

Revision History (Full details and data files)

Version 1.0: 2009-07-28
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

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Deposit Data

Help and Resources

3H9V

Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.1 Angstroms

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)