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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2A IN THE PRESENCE OF EDTA
 
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 :  2.70
Chains :  Asym./Biol. Unit :  A,B,H,L
Keywords :  Ion Channel, Nmda Receptor, Allosteric Modulation, Zinc Inhibition, Immune System, 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 Common: MOUSE
    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, 17)

Asymmetric/Biological Unit (4, 17)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2IPA1Ligand/IonISOPROPYL ALCOHOL
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO412Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:35 , LYS A:36binding site for residue GOL A 503
02AC2SOFTWAREHIS A:146 , LYS A:179 , ASN A:362 , ARG A:367binding site for residue GOL A 504
03AC3SOFTWAREHIS A:38 , ASN A:297 , GLU A:298 , SER A:299 , NAG A:501 , LYS L:147binding site for residue SO4 A 505
04AC4SOFTWAREARG A:358 , NAG A:502 , LYS L:199binding site for residue SO4 A 506
05AC5SOFTWARESER A:245 , GLU A:246 , ARG A:273binding site for residue SO4 A 507
06AC6SOFTWARETHR A:222 , LYS A:223 , ASN A:224binding site for residue SO4 A 508
07AC7SOFTWARETHR A:333 , ASN A:334 , ILE A:335 , ASP B:105 , GLN B:106binding site for residue SO4 A 509
08AC8SOFTWAREASN A:159 , ARG B:244 , SER B:274 , HOH B:502binding site for residue SO4 B 401
09AC9SOFTWAREGLY B:179 , TYR B:180 , ARG B:181 , ASP B:182binding site for residue SO4 B 402
10AD1SOFTWARETHR B:333 , HIS B:335binding site for residue SO4 B 403
11AD2SOFTWAREHIS A:162 , ARG B:244binding site for residue SO4 B 404
12AD3SOFTWARETHR H:182 , LEU H:183 , SER H:184 , LEU L:160 , SER L:162 , SER L:176 , THR L:178binding site for residue IPA H 301
13AD4SOFTWAREARG L:108 , ASP L:170binding site for residue SO4 L 301
14AD5SOFTWARELYS A:37 , GLU L:154 , ARG L:155 , GLN L:156 , ASN L:157binding site for residue SO4 L 302
15AD6SOFTWAREASN A:297 , SO4 A:505 , HOH A:609 , ASN L:145 , LYS L:147 , GLU L:195 , ALA L:196 , THR L:197binding site for Mono-Saccharide NAG A 501 bound to ASN A 297
16AD7SOFTWAREASN A:389 , TYR A:392 , SO4 A:506binding site for Mono-Saccharide NAG A 502 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  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe H:152 -Pro H:153
2Glu H:154 -Pro H:155
3Trp H:194 -Pro H:195
4Phe L:94 -Pro L:95
5Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TQ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TQ0)

(-) Exons   (0, 0)

(no "Exon" information available for 5TQ0)

(-) 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:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               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......hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh.ee.......eee.....ee...eeeeeee..eeeeeeee....ee....eee.....eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tq0 A  24 PKIVNIGAVLSTKKHEQIFREAVNQANKRHRKIQLQATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGGETEGTLVPR 414
                                    33        43        53|       65        75        85        95 ||    108       118       128       138       148       158       168       178       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410    
                                                        53|                                       97|                                                                                   187|                                                                                                                                                                                                            
                                                         56                                       101                                                                                    210                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...............eeeeee....hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh..eeeeehhhhh..........eee...hhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhh....ee...eee.....hhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh.......eeeehhhhhh.............eeee......hhhhhhhhhhhhhhhhhhhhhhhh..........................ee..ee..............eeeee.....eeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tq0 B  34 LNIAVLLGHSHDVTERELPLDVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSQTFIPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGYRDFISFIKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGLGILTTAASSMLEKFSYIPEAKASCYGQTPLHTLHQFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENQTLSLRHA 388
                                    43      ||65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       330       340       350       360       370       380        
                                           50|                                                                                                                                                                                                                                                                 323|                                                           
                                            63                                                                                                                                                                                                                                                                  329                                                           


Chain H from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee....eeeeeeeee.......eeeeeeee..eeeeeeeeee.....eee.hhhh..eeeee.....eeeeeee..hhhhheeeeeeee......eeee...eeeee........eeeee....eeeeeeeeeee.....eeee........eee...ee....eeeeeeeeee.........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tq0 H   1 EVKLVESGPELKKPGETVKISCKASGFTFTNYGMNWVKQAPGKGLKWMGWINIYTGEPTYADDFKGRFAFSLETSASTAYLQINNLKNEDTATYFCARGYDYEGYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   146       156       166       176       186       196       206       216  
                                                                                                                                                              133|                                                                              
                                                                                                                                                               140                                                                              


Chain L from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee......eeee.....eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee...........eeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeehhhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5tq0 L   1 DIVMTQAPATLSVTPGDRVSLSCRASQSIADYLYWYQQKSHESPRLLLKYPSRFSGSGSGSDFTLTINSVEPEDVGMYYCQNGHSFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLAAGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    10        20        30        40        50|       68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    
                                                                            50|                                                                                                                                                         
                                                                             59
   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 5TQ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TQ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TQ0)

(-) Gene Ontology  (71, 85)

Asymmetric/Biological Unit(hide GO term definitions)

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  5tq0
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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 5tq2 5vih 5vii 5vij
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        Q91977_XENLA | Q91977: 3qek 3qel 3qem 5b3j 5ewj 5ewl 5ewm 5tpw 5tpz 5tq2

(-) Related Entries Specified in the PDB File

5tpw 5tpz 5tq2