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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLUR2 LIGAND BINDING CORE (S1S2J) IN COMPLEX WITH QUISQUALATE AND CX614.
 
Authors :  R. Jin, S. Clark, A. M. Weeks, J. T. Dudman, E. Gouaux, K. M. Partin
Date :  04 Aug 05  (Deposition) - 25 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A (1x),B (1x),F (1x)
Biol. Unit 2:  C (1x),D (1x),E (1x)
Keywords :  Ionotropic Glutamate Receptor, Glur2, Ligand Binding Core, S1S2, Quisqualate, Cx614, Modulator, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Jin, S. Clark, A. M. Weeks, J. T. Dudman, E. Gouaux, K. M. Partin
Mechanism Of Positive Allosteric Modulators Acting On Ampa Receptors.
J. Neurosci. V. 25 9027 2005
PubMed-ID: 16192394  |  Reference-DOI: 10.1523/JNEUROSCI.2567-05.2005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR 2
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETGQ
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: LIGAND BINDING CORE (S1S2J)
    Gene: GRIA2, GLUR2
    Mutation: YES
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUR-2, GLUR-B, GLUR-K2, GLUTAMATE RECEPTOR IONOTROPIC, AMPA 2

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A (1x)B (1x)   F (1x)
Biological Unit 2 (1x):   C (1x)D (1x)E (1x) 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
1CX63Ligand/Ion2,3,6A,7,8,9-HEXAHYDRO-11H-[1,4]DIOXINO[2,3-G]PYRROLO[2,1-B][1,3]BENZOXAZIN-11-ONE
2QUS6Ligand/Ion(S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID
3ZN10Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CX6-1Ligand/Ion2,3,6A,7,8,9-HEXAHYDRO-11H-[1,4]DIOXINO[2,3-G]PYRROLO[2,1-B][1,3]BENZOXAZIN-11-ONE
2QUS-1Ligand/Ion(S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CX6-1Ligand/Ion2,3,6A,7,8,9-HEXAHYDRO-11H-[1,4]DIOXINO[2,3-G]PYRROLO[2,1-B][1,3]BENZOXAZIN-11-ONE
2QUS-1Ligand/Ion(S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:42 , HIS A:46 , GLU B:166BINDING SITE FOR RESIDUE ZN A 821
02AC2SOFTWAREHIS B:23 , GLU B:30BINDING SITE FOR RESIDUE ZN B 822
03AC3SOFTWAREASP C:65BINDING SITE FOR RESIDUE ZN C 823
04AC4SOFTWAREGLU B:42 , HIS B:46 , LEU B:241 , GLN B:244 , HOH B:825BINDING SITE FOR RESIDUE ZN B 824
05AC5SOFTWAREGLU C:42 , HIS C:46BINDING SITE FOR RESIDUE ZN C 825
06AC6SOFTWAREGLU D:42 , HIS D:46 , GLU E:166BINDING SITE FOR RESIDUE ZN D 826
07AC7SOFTWAREHIS E:23 , GLU E:30BINDING SITE FOR RESIDUE ZN E 827
08AC8SOFTWAREASP F:65BINDING SITE FOR RESIDUE ZN F 828
09AC9SOFTWAREGLU E:42 , HIS E:46 , LEU E:241 , GLN E:244 , HOH E:832BINDING SITE FOR RESIDUE ZN E 829
10BC1SOFTWAREGLU F:42 , HIS F:46BINDING SITE FOR RESIDUE ZN F 830
11BC2SOFTWAREPRO A:105 , PHE A:106 , MET A:107 , SER A:108 , SER A:217 , LYS A:218 , GLY A:219 , ASN A:242 , HOH A:952 , PRO C:105 , PHE C:106 , MET C:107 , SER C:108 , SER C:217 , LYS C:218 , GLY C:219 , ASN C:242 , HOH C:851 , HOH C:911 , HOH C:934BINDING SITE FOR RESIDUE CX6 C 801
12BC3SOFTWAREPRO B:105 , PHE B:106 , MET B:107 , SER B:108 , SER B:217 , LYS B:218 , GLY B:219 , ASN B:242 , HOH B:967 , PRO E:105 , PHE E:106 , MET E:107 , SER E:108 , SER E:217 , LYS E:218 , GLY E:219 , ASN E:242 , HOH E:830 , HOH E:860 , HOH E:975BINDING SITE FOR RESIDUE CX6 E 802
13BC4SOFTWAREPRO D:105 , PHE D:106 , MET D:107 , SER D:108 , SER D:217 , LYS D:218 , GLY D:219 , ASN D:242 , HOH D:778 , PRO F:105 , PHE F:106 , MET F:107 , SER F:108 , SER F:217 , LYS F:218 , GLY F:219 , ASN F:242 , HOH F:515 , HOH F:706 , HOH F:775BINDING SITE FOR RESIDUE CX6 F 803
14BC5SOFTWARETYR A:61 , PRO A:89 , LEU A:90 , THR A:91 , ARG A:96 , LEU A:138 , GLY A:141 , SER A:142 , THR A:143 , LEU A:192 , GLU A:193 , MET A:196 , HOH A:822 , HOH A:835 , HOH A:841BINDING SITE FOR RESIDUE QUS A 807
15BC6SOFTWARETYR B:61 , PRO B:89 , LEU B:90 , THR B:91 , ARG B:96 , LEU B:138 , GLY B:141 , SER B:142 , THR B:143 , LEU B:192 , GLU B:193 , MET B:196 , HOH B:829 , HOH B:839 , HOH B:850BINDING SITE FOR RESIDUE QUS B 808
16BC7SOFTWARETYR C:61 , PRO C:89 , LEU C:90 , THR C:91 , ARG C:96 , LEU C:138 , GLY C:141 , SER C:142 , THR C:143 , LEU C:192 , GLU C:193 , MET C:196 , HOH C:829 , HOH C:837 , HOH C:865BINDING SITE FOR RESIDUE QUS C 809
17BC8SOFTWARETYR D:61 , PRO D:89 , LEU D:90 , THR D:91 , ARG D:96 , LEU D:138 , GLY D:141 , SER D:142 , THR D:143 , LEU D:192 , GLU D:193 , MET D:196 , HOH D:392 , HOH D:428 , HOH D:455BINDING SITE FOR RESIDUE QUS D 810
18BC9SOFTWARETYR E:61 , PRO E:89 , LEU E:90 , THR E:91 , ARG E:96 , LEU E:138 , GLY E:141 , SER E:142 , THR E:143 , LEU E:192 , GLU E:193 , MET E:196 , HOH E:836 , HOH E:846 , HOH E:857BINDING SITE FOR RESIDUE QUS E 811
19CC1SOFTWARETYR F:61 , PRO F:89 , LEU F:90 , THR F:91 , ARG F:96 , LEU F:138 , GLY F:141 , SER F:142 , THR F:143 , LEU F:192 , GLU F:193 , MET F:196 , HOH F:417 , HOH F:448 , HOH F:557BINDING SITE FOR RESIDUE QUS F 812

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:206 -A:261
2B:206 -B:261
3C:206 -C:261
4D:206 -D:261
5E:206 -E:261
6F:206 -F:261

(-) Cis Peptide Bonds  (18, 18)

Asymmetric Unit
No.Residues
1Ser A:14 -Pro A:15
2Glu A:166 -Pro A:167
3Lys A:204 -Pro A:205
4Ser B:14 -Pro B:15
5Glu B:166 -Pro B:167
6Lys B:204 -Pro B:205
7Ser C:14 -Pro C:15
8Glu C:166 -Pro C:167
9Lys C:204 -Pro C:205
10Ser D:14 -Pro D:15
11Glu D:166 -Pro D:167
12Lys D:204 -Pro D:205
13Ser E:14 -Pro E:15
14Glu E:166 -Pro E:167
15Lys E:204 -Pro E:205
16Ser F:14 -Pro F:15
17Glu F:166 -Pro F:167
18Lys F:204 -Pro F:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AL4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AL4)

(-) Exons   (0, 0)

(no "Exon" information available for 2AL4)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:258
 aligned with GRIA2_RAT | P19491 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:381
                                   423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793 
            GRIA2_RAT   414 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 794
               SCOP domains d2al4a_ A: Glutamate receptor ligand binding core                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2al4A01 A:4-109,A:219-261 Periplasmic binding protein-like II                                             2al4A02 A                                                                                                                           :110-218 Periplasmic binding protein-like II                                                        2al4A01 A:4-109,A:219-261                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee..---------------------------------------------------------------------------------------------------------------------------....hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2al4 A   4 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKG---------------------------------------------------------------------------------------------------------------------------TPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 261
                                    13        23        33        43        53        63        73        83        93       103       113    |    -         -         -         -         -         -         -         -         -         -         -         -       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
                                                                                                                                            118                                                                                                                         119                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:259
 aligned with GRIA2_RAT | P19491 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:382
                                   422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792  
            GRIA2_RAT   413 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 794
               SCOP domains d2al4b_ B: Glutamate receptor ligand binding core                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2al4B01 B:3-109,B:219-261 Periplasmic binding protein-like II                                              2al4B02 B                                                                                                                           :110-218 Periplasmic binding protein-like II                                                        2al4B01 B:3-109,B:219-261                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......ee........hhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee..---------------------------------------------------------------------------------------------------------------------------....hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhh......eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2al4 B   3 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKG---------------------------------------------------------------------------------------------------------------------------TPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 261
                                    12        22        32        42        52        62        72        82        92       102       112     |   -         -         -         -         -         -         -         -         -         -         -         -       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259  
                                                                                                                                             118                                                                                                                         119                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:258
 aligned with GRIA2_RAT | P19491 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:381
                                   423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793 
            GRIA2_RAT   414 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 794
               SCOP domains d2al4c_ C: Glutamate receptor ligand binding core                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2al4C01 C:4-109,C:219-261 Periplasmic binding protein-like II                                             2al4C02 C                                                                                                                           :110-218 Periplasmic binding protein-like II                                                        2al4C01 C:4-109,C:219-261                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee..---------------------------------------------------------------------------------------------------------------------------....hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2al4 C   4 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKG---------------------------------------------------------------------------------------------------------------------------TPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 261
                                    13        23        33        43        53        63        73        83        93       103       113    |    -         -         -         -         -         -         -         -         -         -         -         -       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
                                                                                                                                            118                                                                                                                         119                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:258
 aligned with GRIA2_RAT | P19491 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:381
                                   423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793 
            GRIA2_RAT   414 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 794
               SCOP domains d2al4d_ D: Glutamate receptor ligand binding core                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2al4D01 D:4-109,D:219-261 Periplasmic binding protein-like II                                             2al4D02 D                                                                                                                           :110-218 Periplasmic binding protein-like II                                                        2al4D01 D:4-109,D:219-261                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee..---------------------------------------------------------------------------------------------------------------------------....hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2al4 D   4 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKG---------------------------------------------------------------------------------------------------------------------------TPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 261
                                    13        23        33        43        53        63        73        83        93       103       113    |    -         -         -         -         -         -         -         -         -         -         -         -       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
                                                                                                                                            118                                                                                                                         119                                                                                                                                              


Chain E from PDB  Type:PROTEIN  Length:259
 aligned with GRIA2_RAT | P19491 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:382
                                   422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792  
            GRIA2_RAT   413 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 794
               SCOP domains d2al4e_ E: Glutamate receptor ligand binding core                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2al4E01 E:3-109,E:219-261 Periplasmic binding protein-like II                                              2al4E02 E                                                                                                                           :110-218 Periplasmic binding protein-like II                                                        2al4E01 E:3-109,E:219-261                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......ee........hhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee..---------------------------------------------------------------------------------------------------------------------------....hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhh......eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2al4 E   3 NKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKG---------------------------------------------------------------------------------------------------------------------------TPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 261
                                    12        22        32        42        52        62        72        82        92       102       112     |   -         -         -         -         -         -         -         -         -         -         -         -       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259  
                                                                                                                                             118                                                                                                                         119                                                                                                                                              


Chain F from PDB  Type:PROTEIN  Length:258
 aligned with GRIA2_RAT | P19491 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:381
                                   423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793 
            GRIA2_RAT   414 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 794
               SCOP domains d2al4f_ F: Glutamate receptor ligand binding core                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2al4F01 F:4-109,F:219-261 Periplasmic binding protein-like II                                             2al4F02 F                                                                                                                           :110-218 Periplasmic binding protein-like II                                                        2al4F01 F:4-109,F:219-261                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......ee..hhhhhhhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee..---------------------------------------------------------------------------------------------------------------------------....hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh...eeeeeehhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2al4 F   4 KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKG---------------------------------------------------------------------------------------------------------------------------TPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNKWWYDKGEC 261
                                    13        23        33        43        53        63        73        83        93       103       113    |    -         -         -         -         -         -         -         -         -         -         -         -       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
                                                                                                                                            118                                                                                                                         119
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 12)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: D-Maltodextrin-Binding Protein; domain 2 (600)
(-)
Homologous Superfamily: Periplasmic binding protein-like II (486)
(-)
Norway rat (Rattus norvegicus) (84)
1a2al4A01A:4-109,A:219-261
1b2al4A02A:110-218
1c2al4B02B:110-218
1d2al4C02C:110-218
1e2al4D02D:110-218
1f2al4E02E:110-218
1g2al4F02F:110-218
1h2al4C01C:4-109,C:219-261
1i2al4D01D:4-109,D:219-261
1j2al4F01F:4-109,F:219-261
1k2al4B01B:3-109,B:219-261
1l2al4E01E:3-109,E:219-261

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AL4)

(-) Gene Ontology  (49, 49)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (GRIA2_RAT | P19491)
molecular function
    GO:0004971    AMPA glutamate receptor activity    An ionotropic glutamate receptor activity that exhibits fast gating by glutamate and acts by opening a cation channel permeable to sodium, potassium, and, in the absence of a GluR2 subunit, calcium.
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0005246    calcium channel regulator activity    Modulates the activity of a calcium channel.
    GO:0005234    extracellular-glutamate-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when extracellular glutamate has been bound by the channel complex or one of its constituent parts.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    GO:0004970    ionotropic glutamate receptor activity    Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts.
    GO:0015277    kainate selective glutamate receptor activity    An ionotropic glutamate receptor activity that exhibits fast gating by glutamate, acts by opening a cation channel permeable to sodium and potassium, and for which kainate is an agonist.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0045184    establishment of protein localization    The directed movement of a protein to a specific location.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0035235    ionotropic glutamate receptor signaling pathway    A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0050806    positive regulation of synaptic transmission    Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0031623    receptor internalization    A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane.
    GO:0001919    regulation of receptor recycling    Any process that modulates the frequency, rate, or extent of receptor recycling.
    GO:0051966    regulation of synaptic transmission, glutamatergic    Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.
    GO:0060992    response to fungicide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fungicide stimulus. Fungicides are chemicals used to kill fungi.
    GO:0010226    response to lithium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lithium (Li+) ion stimulus.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0032281    AMPA glutamate receptor complex    An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. The AMPA receptors mediate fast synaptic transmission in the CNS and are composed of subunits GluR1-4, products from separate genes. These subunits have an extracellular N-terminus and an intracellular C-terminus.
    GO:0032279    asymmetric synapse    A type of synapse occurring between an axon and a dendritic spine or dendritic shaft. Asymmetric synapses, the most abundant synapse type in the central nervous system, involve axons that contain predominantly spherical vesicles and contain a thickened postsynaptic density. Most or all synapses of this type are excitatory.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0032839    dendrite cytoplasm    All of the contents of a dendrite, excluding the surrounding plasma membrane.
    GO:0043198    dendritic shaft    Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0008328    ionotropic glutamate receptor complex    A multimeric assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand-gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0042734    presynaptic membrane    A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0030672    synaptic vesicle membrane    The lipid bilayer surrounding a synaptic vesicle.
    GO:0043195    terminal bouton    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.

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  2al4
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  GRIA2_RAT | P19491
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GRIA2_RAT | P19491: 1ftj 1ftk 1ftl 1ftm 1fto 1fw0 1gr2 1lb8 1lb9 1lbb 1lbc 1m5b 1m5c 1m5d 1m5e 1m5f 1mm6 1mm7 1mqd 1mqg 1mqh 1mqi 1mqj 1ms7 1mxu 1mxv 1mxw 1mxx 1mxy 1mxz 1my0 1my1 1my2 1my3 1my4 1n0t 1nnk 1nnp 1p1n 1p1o 1p1q 1p1u 1p1w 1syh 1syi 1wvj 1xhy 2aix 2al5 2anj 2cmo 2gfe 2i3v 2i3w 2p2a 2uxa 2xx7 2xx8 2xx9 2xxh 2xxi 3b6q 3b6t 3b6w 3b7d 3bbr 3bft 3bfu 3bki 3dp6 3h03 3h06 3h5v 3h5w 3h6t 3h6u 3h6v 3h6w 3hsy 3ijo 3ijx 3ik6 3il1 3ilt 3ilu 3kg2 3kgc 3lsf 3lsl 3m3l 3n6v 3o28 3o29 3o2a 3o2j 3o6g 3o6h 3o6i 3pd8 3pd9 3pmv 3pmw 3pmx 3rtf 3rtw 3t93 3t96 3t9h 3t9u 3t9v 3t9x 3tdj 3tkd 3tza 4fat 4g8m 4gxs 4h8j 4igt 4isu 4iy5 4iy6 4l17 4lz5 4lz7 4lz8 4n07 4o3a 4o3b 4o3c 4q30 4u1o 4u1w 4u1x 4u1y 4u1z 4u21 4u22 4u23 4u2p 4u2q 4u2r 4u4f 4u4g 4u4s 4u4x 4u5b 4u5c 4u5d 4u5e 4u5f 4uq6 4uqj 4uqk 4x48 4yma 4yu0 4z0i 5buu 5cbr 5cbs 5elv 5fhm 5fhn 5fho 5fth 5fti 5fwx 5fwy 5ide 5idf 5jei 5kbs 5kbt 5kbu 5kbv 5kk2 5l1b 5l1e 5l1f 5l1g 5l1h 5vhw 5vhx 5vhy 5vhz 5vot 5vou 5vov

(-) Related Entries Specified in the PDB File

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1mm6 GLUR2 LIGAND BINDING CORE IN COMPLEX WITH QUISQUALATE
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2al5