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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2A IN COMPLEX WITH ZINC AT GLUN1 AND GLUN2A
 
Authors :  A. Romero-Hernandez, N. Simorowski, E. Karakas, H. Furukawa
Date :  21 Oct 16  (Deposition) - 14 Dec 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.29
Chains :  Asym./Biol. Unit :  A,B,H,L
Keywords :  Ion Channel, Nmda Receptor, Allosteric Modulation, Zinc Inhibition, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Romero-Hernandez, N. Simorowski, E. Karakas, H. Furukawa
Molecular Basis For Subtype Specificity And High-Affinity Zinc Inhibition In The Glun1-Glun2A Nmda Receptor Amino-Terminal Domain
Neuron V. 92 1 2016
PubMed: search  |  Reference-DOI: 10.1016/J.NEURON.2016.11.006

(-) Compounds

Molecule 1 - NMDA GLUTAMATE RECEPTOR SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: RESIDUES 24-408
    Gene: GRIN1, NR1
    Mutation: YES
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
 
Molecule 2 - GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2A
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: RESIDUES 34-393
    Gene: GRIN2A
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUN2A,GLUTAMATE [NMDA] RECEPTOR SUBUNIT EPSILON-1,N-METHYL D-ASPARTATE RECEPTOR SUBTYPE 2A,NR2A
 
Molecule 3 - FAB, HEAVY CHAIN
    Chains: H
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 4 - FAB, LIGHT CHAIN
    Chains: L
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO44Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:67 , HIS A:94 , ASP A:100 , HOH A:602binding site for residue ZN A 501
2AC2SOFTWAREARG A:358 , NAG A:503 , LYS L:199binding site for residue SO4 A 504
3AC3SOFTWAREHIS A:38 , ASN A:297 , GLU A:298 , SER A:299 , NAG A:502binding site for residue SO4 A 505
4AC4SOFTWARETHR A:55 , LYS A:57 , ALA L:7 , PRO L:8 , ALA L:9binding site for residue SO4 A 506
5AC5SOFTWARELYS A:36binding site for residue GOL A 507
6AC6SOFTWAREHIS B:44 , HIS B:128 , GLU B:266 , ASP B:282binding site for residue ZN B 401
7AC7SOFTWAREASN A:159 , ARG B:244 , SER B:274 , ARG B:370binding site for residue SO4 B 402
8AC8SOFTWAREASN A:297 , SER A:299 , SO4 A:505 , LYS L:147 , GLU L:195 , THR L:197binding site for Mono-Saccharide NAG A 502 bound to ASN A 297
9AC9SOFTWAREASN A:389 , SO4 A:504binding site for Mono-Saccharide NAG A 503 bound to ASN A 389

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:79 -A:329
2B:87 -B:320
3H:22 -H:96
4H:146 -H:201
5L:23 -L:88
6L:134 -L:194

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:152 -Pro H:153
2Ala L:7 -Pro L:8
3Phe L:94 -Pro L:95
4Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TQ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TQ2)

(-) Exons   (0, 0)

(no "Exon" information available for 5TQ2)

(-) 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:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee...hhhhhhhhhhhhhhhh.eeeeee...........hhhhhhhhhhh...eee....hhhhhh......eee...hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh.......eee.......hhhhhh.....eeeee....hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh.ee.......eee.....ee...eeeeee....eeeeeee....eee....ee.....ee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tq2 A  24 PKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGGETEGTLV 412
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183  ||   217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407     
                                                                                                                                                                                            186|                                                                                                                                                                                                         
                                                                                                                                                                                             211                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhh.....eeeeee....hhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhh..eeeeehhhhh..........eee...hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh........eee.......hhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh......eeeehhhhhh.............eeee......hhhhhhhhhhhhhhhhhhhh.....................hhhhhh.eee..eee.............eeeee.....eee................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tq2 B  34 LNIAVLLGHSHDVTEREVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSQTFIPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGYRDFISFIKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGLGILTTAASSMLEKFSYIPEAKASCYGQPLHTLHQFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENQTLSLRHAVW 390
                                    43      ||69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319   ||  335       345       355       365       375       385     
                                           50|                                                                                                                                                                                                                                                             323|                                                            
                                            67                                                                                                                                                                                                                                                              330                                                            


Chain H from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...ee......eeeeeeee..hhhhheeeeeee......eeeeee......eee.hhhh..ee..ee....eeeeee...hhhhh.eeeeeee.hhh..eeee...eeee.........eeeee.......eeeeeee.....................ee....eeeee..........eee..........eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tq2 H   1 EVKLVESGPELKKPGETVKISCKASGFTFTNYGMNWVKQAPGKGLKWMGWINIYTGEPTYADDFKGRFAFSLETSASTAYLQINNLKNEDTATYFCARGYDYEGYFDYWGQGTTLTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSHTFPAVLQSDLYTLSSSPSSTWPETVTCNVAHPASSTKVDKKIVP 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 ||    147       157       167|      179      |192  ||   203       213     
                                                                                                                                                             132|                        167|             186|  195|                     
                                                                                                                                                              140                         170              190   197                     


Chain L from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee...........eeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeee.hhhhhh....eeeeee..........ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tq2 L   1 DIVMTQAPATLSVTPGDRVSLSCRASQSIADYLYWYQQKSHESPRLLLKYAIPSRFSGSGSGSDFTLTINSVEPEDVGMYYCQNGHSFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLAAGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSF 209
                                    10        20        30        40        50||      66        76        86        96       106       116       126 ||    137       147       157       167       177       187       197       207  
                                                                             51|                                                                   128|                                                                               
                                                                              58                                                                    130
   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  (0, 0)

(no "SCOP Domain" information available for 5TQ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TQ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TQ2)

(-) Gene Ontology  (71, 85)

Asymmetric/Biological Unit(hide GO term definitions)

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  5tq2
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  Q91977_XENLA | Q91977
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 Related Entries

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

UniProtKB/Swiss-Prot
        NMDE1_RAT | Q00959: 2a5s 2a5t 4jwx 4nf4 4nf5 4nf6 4nf8 5ddn 5ddx 5de4 5dex 5i56 5i57 5i58 5i59 5jty 5tpw 5tq0 5vih 5vii 5vij
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        Q91977_XENLA | Q91977: 3qek 3qel 3qem 5b3j 5ewj 5ewl 5ewm 5tpw 5tpz 5tq0

(-) Related Entries Specified in the PDB File

5tpw 5tpz 5tq0