3FAT: IGluR4 flip ligand-binding core

X-ray structure of iGluR4 flip ligand-binding core (S1S2) in complex with (S)-AMPA at 1.90A resolution. Determined by X-ray diffraction at 1.9 Å resolution. Released 9 Dec 2008.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Rattus norvegicus
Chains: 3
Atoms: 6,962
Mol. weight: 89.48 kDa
Ligands: AMQ
Released: 9 Dec 2008

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

Secondary structure: helices and β-sheets

3FAT contains 46 α-helices and 60 β-strands across 3 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	3-8	6	1
β-strand	11	1	2
β-strand	15	1	2
β-strand	16-17	2	3
α-helix	18	1
α-helix	21-23	3
α-helix	26-29	4
β-strand	30-31	2	3
α-helix	33-45	13
β-strand	48-53	6	1
β-strand	62	1	4
β-strand	69	1	4
α-helix	71-77	7
β-strand	83-84	2	1
β-strand	89	1	5
α-helix	92-95	4
β-strand	98-100	3	1
α-helix	101	1
α-helix	103	1
β-strand	105-107	3	5
β-strand	109-114	6	6
α-helix	122-126	5
β-strand	132-135	4	6
β-strand	136	1	7
α-helix	140-147	8
α-helix	151-161	11
β-strand	169	1	7
α-helix	172-181	10
β-strand	186-191	6	6
α-helix	192-199	8
β-strand	206-209	4	6
β-strand	216-218	3	5
β-strand	221-223	3	1
α-helix	229-241	13
α-helix	244-253	10

Chain B: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
β-strand	3-8	6	8
β-strand	11	1	9
β-strand	15	1	9
β-strand	16-17	2	10
α-helix	21-23	3
α-helix	26-29	4
β-strand	30-31	2	10
α-helix	33-45	13
β-strand	48-53	6	8
β-strand	62	1	11
β-strand	69	1	11
α-helix	71-77	7
β-strand	83-84	2	8
β-strand	89	1	12
α-helix	92-95	4
β-strand	98-100	3	8
α-helix	101	1
α-helix	103	1
β-strand	105-107	3	12
β-strand	109-114	6	13
α-helix	122-127	6
β-strand	132-135	4	13
β-strand	136	1	14
α-helix	140-147	8
α-helix	151-162	12
β-strand	169	1	14
α-helix	172-181	10
β-strand	186-191	6	13
α-helix	192-199	8
β-strand	206-209	4	13
β-strand	216-218	3	12
β-strand	221-223	3	8
α-helix	229-241	13
α-helix	244-253	10

Chain C: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
β-strand	3-8	6	15
β-strand	11	1	16
β-strand	15	1	16
β-strand	16-17	2	17
α-helix	18	1
α-helix	21-23	3
α-helix	26-29	4
β-strand	30-31	2	17
α-helix	33-45	13
β-strand	48-53	6	15
β-strand	62	1	18
β-strand	69	1	18
α-helix	71-78	8
β-strand	83-84	2	15
β-strand	89	1	19
α-helix	92-95	4
β-strand	98-100	3	15
α-helix	101	1
α-helix	103	1
β-strand	105-107	3	19
β-strand	109-114	6	20
α-helix	122-126	5
β-strand	132-135	4	20
β-strand	136	1	21
α-helix	140-147	8
α-helix	151-161	11
β-strand	169	1	21
α-helix	172-181	10
β-strand	186-191	6	20
α-helix	192-199	8
β-strand	206-209	4	20
β-strand	216-218	3	19
β-strand	221-223	3	15
α-helix	229-241	13
α-helix	244-253	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 4	A, B, C	protein	260	Rattus norvegicus	P19493 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>3FAT_1 Glutamate receptor 4 (chains A, B, C)
GRTVVVTTIMESPYVMYKKNHEMFEGNDKYEGYCVDLASEIAKHIGIKYKIAIVPDGKYG
ARDADTKIWNGMVGELVYGKAEIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIE
SAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMRSAEPSVFTRTTAEGVARVR
KSKGKFAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGVATPKGSSLRTPVNLAVLKLS
EAGVLDKLKNKWWYDKGECG

Ligands and cofactors

ID	Name	Formula	Copies
AMQ	(s)-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid	C7 H10 N2 O4	3

Water and common crystallization additives (ACY, GOL, SO4) are not listed.

Primary citation

Molecular mechanism of agonist recognition by the ligand-binding core of the ionotropic glutamate receptor 4. Kasper, C., Frydenvang, K., Naur, P. et al. FEBS Lett (2008) 582:4089-4094. DOI 10.1016/j.febslet.2008.11.005 · 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…
3EPE 1.85 Å, Crystal Structure of the GluR4 Ligand-Binding domain in complex with glutamate
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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