3EPE: GluR4 Ligand-Binding domain

Crystal Structure of the GluR4 Ligand-Binding domain in complex with glutamate. Determined by X-ray diffraction at 1.85 Å resolution. Released 19 May 2009.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 4,358
Mol. weight: 57.77 kDa
Ligands: GLU
Released: 19 May 2009

Explore 3EPE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EPE contains 31 α-helices and 39 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	9	1	2
β-strand	13	1	2
β-strand	14-15	2	3
α-helix	19-21	3
α-helix	24-27	4
β-strand	28-29	2	3
α-helix	31-43	13
β-strand	47-51	5	1
β-strand	60	1	4
β-strand	67	1	4
α-helix	69-75	7
β-strand	81-82	2	1
β-strand	87	1	5
α-helix	90-93	4
β-strand	96-98	3	1
α-helix	99	1
α-helix	101	1
β-strand	103-105	3	5
β-strand	107-112	6	6
α-helix	120-124	5
β-strand	130-133	4	6
β-strand	134	1	7
α-helix	138-145	8
α-helix	149-160	12
β-strand	167	1	7
α-helix	170-179	10
β-strand	184-189	6	6
α-helix	190-197	8
β-strand	204-207	4	6
β-strand	214-216	3	5
β-strand	219-221	3	1
α-helix	227-239	13
α-helix	242-247	6
α-helix	248-252	5

Chain B: 16 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
β-strand	9	1	9
β-strand	13	1	9
β-strand	14-15	2	10
α-helix	16	1
α-helix	19-21	3
α-helix	24-27	4
β-strand	28-29	2	10
α-helix	31-43	13
β-strand	47-51	5	8
β-strand	60	1	11
β-strand	67	1	11
α-helix	69-75	7
β-strand	81-82	2	8
β-strand	87	1	12
α-helix	90-93	4
β-strand	96-98	3	8
α-helix	99	1
α-helix	101	1
β-strand	103-105	3	12
β-strand	107-112	6	13
α-helix	120-124	5
β-strand	130-134	5	13
α-helix	138-145	8
α-helix	149-160	12
β-strand	166-167	2	13
α-helix	170-179	10
β-strand	184-189	6	13
α-helix	190-197	8
β-strand	204-207	4	13
β-strand	214-216	3	12
β-strand	219-221	3	8
α-helix	227-239	13
α-helix	242-247	6
α-helix	248-253	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 4,Glutamate receptor	A, B	protein	257	Rattus norvegicus	P19493 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3EPE_1 Glutamate receptor 4,Glutamate receptor (chains A, B)
TVVVTTIMESPYVMYKKNHEMFEGNDKYEGYCVDLASEIAKHIGIKYKIAIVPDGKYGAR
DADTKIWNGMVGELVYGKAEIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIESA
EDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMRSAEPSVFTRTTAEGVARVRKS
KGKFAFLLESTMNEYTEQRKPCDTMKVGGNLDSKGYGVATPKGSSLRTPVNLAVLKLSEA
GVLDKLKNKWWYDKGEC

Ligands and cofactors

ID	Name	Formula	Copies
GLU	Glutamic acid	C5 H9 N O4	2

Primary citation

Correlating AMPA receptor activation and cleft closure across subunits: crystal structures of the GluR4 ligand-binding domain in complex with full and partial agonists. Gill, A., Birdsey-Benson, A., Jones, B.L. et al. Biochemistry (2008) 47:13831-13841. DOI 10.1021/bi8013196 · PubMed

Other PDB entries of the same protein (UniProt P19493 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FAS 1.4 Å, X-ray structure of iGluR4 flip ligand-binding core (S1S2) in complex with (S)-glutamate…
3FAT 1.9 Å, X-ray structure of iGluR4 flip ligand-binding core (S1S2) in complex with (S)-AMPA at…
3KEI 1.9 Å, Crystal Structure of the GluA4 Ligand-Binding domain L651V mutant in complex with…
3KFM 2.2 Å, Crystal Structure of the GluA4 Ligand-Binding domain L651V mutant in complex with kainate
4GPA 2.25 Å, High resolution structure of the GluA4 N-terminal domain (NTD)
3EN3 2.43 Å, Crystal Structure of the GluR4 Ligand-Binding domain in complex with kainate
5FWX 2.5 Å, Crystal structure of the AMPA receptor GluA2/A4 N-terminal domain heterodimer
9QDN 2.71 Å, GluA4 in complex with TARP-2, resting state I, structure of TMD/LBD
9RMW 2.9 Å, GluA4 in complex with TARP-2, open state, structure of TMD/LBD domains
9RN7 3.1 Å, GluA4 in complex with TARP-2, Desensitized state, structure of TMD domain
9NR6 3.26 Å, The structure of Noelin 1 with cerebellar GluA1/A4-ATD
9P9B 3.31 Å, Activated GluA4 homotetrameric AMPAR.

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