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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLUK2EM LBD DIMER ASSEMBLY COMPLEX WITH GLUTAMATE AND LY466195
 
Authors :  S. Chittori, M. L. Mayer
Date :  16 Jul 15  (Deposition) - 20 Jul 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Membrane Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Meyerson, S. Chittori, A. Merk, P. Rao, T. H. Han, M. Serpe, M. L. Mayer, S. Subramaniam
Structural Basis Of Kainate Subtype Glutamate Receptor Desensitization.
Nature V. 537 567 2016
PubMed-ID: 27580033  |  Reference-DOI: 10.1038/NATURE19352

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, KAINATE 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22
    Expression System Strain: ORIGAMI B(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 429-544, 667-806
    Gene: GRIK2, GLUR6
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUK2,GLUTAMATE RECEPTOR 6,GLUR6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GLU1Mod. Amino AcidGLUTAMIC ACID
3LI2Ligand/IonLITHIUM ION
4LY51Ligand/Ion(3S,4AR,6S,8AR)-6-{[(2S)-2-CARBOXY-4,4-DIFLUOROPYRROLIDIN-1-YL]METHYL}DECAHYDROISOQUINOLINE-3-CARBOXYLIC ACID
5SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:61 , PRO A:89 , LEU A:90 , THR A:91 , ARG A:96 , GLY A:141 , SER A:142 , THR A:143 , GLU A:191 , HOH A:414 , HOH A:437 , HOH A:448 , HOH A:496binding site for residue GLU A 301
2AC2SOFTWAREGLU A:97 , ILE A:100 , ASP A:101 , HOH A:410binding site for residue LI A 302
3AC3SOFTWARELYS A:104 , HOH A:434 , LYS B:104 , HOH B:468binding site for residue CL A 303
4AC4SOFTWARETYR B:61 , PRO B:89 , LEU B:90 , THR B:91 , ARG B:96 , GLY B:141 , SER B:142 , THR B:143 , SER B:174 , MET B:190 , GLU B:191 , TYR B:217 , HOH B:515 , HOH B:532 , HOH B:568binding site for residue LY5 B 301
5AC5SOFTWAREGLU B:97 , ILE B:100 , ASP B:101 , HOH B:418binding site for residue LI B 302
6AC6SOFTWAREARG A:201 , PRO B:25 , LEU B:26 , HOH B:405 , HOH B:433 , HOH B:605binding site for residue SO4 B 303
7AC7SOFTWAREARG A:31 , ARG A:54 , LEU A:55 , GLU B:57 , HOH B:490binding site for residue SO4 B 304
8AC8SOFTWARELYS A:60 , LYS A:172 , ASN B:3binding site for residue CL B 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CMK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:14 -Pro A:15
2Glu B:14 -Pro B:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CMK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CMK)

(-) Exons   (0, 0)

(no "Exon" information available for 5CMK)

(-) Sequences/Alignments

Asymmetric/Biological 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:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.eeeeeehhhhhhhhh....eeee......eee..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5cmk A   3 NRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVEDGSTMTFFKKSKISTYDKMWAFMSSRRQSVLVKSSEEGIQRVLTSDYALLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRE 301
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252||
                                                                                                                                                                                                                                                                                    253|
                                                                                                                                                                                                                                                                                     301


Chain B from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee................hhhhhhhhh....eeeeeee.hhhhhh.eee....eee.eeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.eeeeeehhhhhhhhh....eeee......eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cmk B   2 SNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVEDGSTMTFFKKSKISTYDKMWAFMSSRRQSVLVKSSEEGIQRVLTSDYALLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRG 254
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 5CMK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CMK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CMK)

(-) Gene Ontology  (52, 52)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        GRIK2_RAT | P42260: 1s50 1s7y 1s9t 1sd3 1tt1 1yae 2i0b 2i0c 2xxr 2xxt 2xxu 2xxv 2xxw 2xxx 2xxy 3g3f 3g3g 3g3h 3g3i 3g3j 3g3k 3h6g 3h6h 3qlt 3qlu 3qlv 4bdl 4bdm 4bdn 4bdo 4bdq 4bdr 4h8i 4uqq 5cmm 5kuf 5kuh

(-) Related Entries Specified in the PDB File

2qs4 GLUK1 LBD COMPLEX WITH LY466195
3g3f GLUK2 LBD COMPLEX WITH GLUTAMATE
4uqq FULL LENGTH GLUK2 EM DESENSITIZED STATE COMPLEX WITH 2S,4R-4- METHYLGLUTAMATE
5cmm