4YU0 | pdb_00004yu0

Crystal structure of a tetramer of GluA2 TR mutant ligand binding domains bound with glutamate at 1.26 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb4YU0/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-03-18 Released: 2016-01-13
Deposition Author(s): Chebli, M., Salazar, H., Baranovic, J., Carbone, A.L., Ghisi, V., Faelber, K., Lau, A.Y., Daumke, O., Plested, A.J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free:
0.157 (Depositor), 0.158 (DCC)
R-Value Work:
0.129 (Depositor), 0.131 (DCC)
R-Value Observed:
0.131 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of the tetrameric GluA2 ligand-binding domain in complex with glutamate at 1.26 Angstroms resolution

Chebli, M., Salazar, H., Baranovic, J., Carbone, A.L., Ghisi, V., Faelber, K., Lau, A.Y., Daumke, O., Plested, A.J.R.

To be published.

Macromolecule Content

Total Structure Weight: 59.66 kDa
Atom Count: 5,112
Modeled Residue Count: 518
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2,Glutamate receptor 2	A, B	263	Rattus norvegicus	Mutation(s): 2 Gene Names: Gria2, Glur2
UniProt
Find proteins for P19491 (Rattus norvegicus) Explore P19491 Go to UniProtKB: P19491
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19491
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLU Query on GLU Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], M [auth B], N [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] J [auth B] K [auth B] D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free: 0.157 (Depositor), 0.158 (DCC)
R-Value Work: 0.129 (Depositor), 0.131 (DCC)
R-Value Observed: 0.131 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.14	α = 90
b = 47.42	β = 93.59
c = 116.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
PHASER	phasing
Coot	model building
XDS	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 2.0: 2021-03-31
Changes: Advisory, Atomic model, Data collection, Derived calculations
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 2.2: 2024-11-13
Changes: Structure summary