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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 THE 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 :  2.91
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, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO46Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:358 , NAG A:502 , LYS L:199binding site for residue SO4 A 503
02AC2SOFTWAREHIS A:38 , ASN A:297 , GLU A:298 , SER A:299 , NAG A:501binding site for residue SO4 A 504
03AC3SOFTWARETHR A:222 , LYS A:223 , ASN A:224binding site for residue SO4 A 505
04AC4SOFTWARETHR A:35 , LYS A:36binding site for residue GOL A 506
05AC5SOFTWAREHIS A:146 , LYS A:179 , GLU A:363 , LYS A:368 , HOH A:602binding site for residue GOL A 507
06AC6SOFTWAREHIS B:44 , HIS B:128 , GLU B:266 , ASP B:282binding site for residue ZN B 401
07AC7SOFTWAREGLY B:179 , TYR B:180 , ARG B:181 , ASP B:182binding site for residue SO4 B 402
08AC8SOFTWAREASN A:159 , ARG B:244 , PRO B:273 , SER B:274 , ARG B:370binding site for residue SO4 B 403
09AC9SOFTWARETHR B:333 , HIS B:335 , GLN B:336binding site for residue SO4 B 404
10AD1SOFTWAREASN A:297 , SO4 A:504 , ASN L:145 , LYS L:149 , GLU L:195 , ALA L:196 , THR L:197binding site for Mono-Saccharide NAG A 501 bound to ASN A 297
11AD2SOFTWAREASN A:389 , SO4 A:503binding 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
2Trp H:194 -Pro H:195
3Ala L:7 -Pro L:8
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 5TPW)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TPW)

(-) 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:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               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.hhhhhhhhhhhhh.........eee..hhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh.eeeee..eeeee.....ee...eeeeeee..eeeeeeee....eee....ee.....ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tpw A  24 PKIVNIGAVLSTKKHEQIFREAVNQANKRHRKIQLQATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFNGSYIIQNDRKIIWPGGETEGTLV 412
                                    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:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..........eeeeee....hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhh..eeeeehhhhh..........eee...hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.....ee...ee.....hhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh.......eeeehhhhhh.............eeee......hhhhhhhhhhhhhhhhhhhh.............................ee..ee..............eeeeee...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tpw B  34 LNIAVLLGHSHDVTEDVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSQTFIPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGYRDFISFIKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGLGILTTAASSMLEKFSYIPEAKASCYGTPLHTLHQFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENQTLSLRH 387
                                    43    ||  70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320 ||    336       346       356       366       376       386 
                                         48|                                                                                                                                                                                                                                                             322|                                                          
                                          66                                                                                                                                                                                                                                                              329                                                          


Chain H from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee....eeeeeeeee..hhhh.eeeeeee.....eeeeeeee.....eee.......eeeeee....eeeeeee..hhhhheeeeeeee......eeee...eeeee.........eeee...eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhh.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tpw H   1 EVKLVESGPELKKPGETVKISCKASGFTFTNYGMNWVKQAPGKGLKWMGWINIYTGEPTYADDFKGRFAFSLETSASTAYLQINNLKNEDTATYFCARGYDYEGYFDYWGQGTTLTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 ||    147       157       167       177       187       197       207       217 
                                                                                                                                                             132|                                                                              
                                                                                                                                                              140                                                                              


Chain L from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......ee.........eeeee...eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh...eeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeehhhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tpw L   1 DIVMTQAPATLSVTPGDRVSLSCRASQSIADYLYWYQQKSHESPRLLLKYASPSRFSGSGSGSDFTLTINSVEPEDVGMYYCQNGHSFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLAAGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    10        20        30        40        50 ||     66        76        86        96       106       116       126       136       146       156       166       176       186       196       206      
                                                                              52|                                                                                                                                                         
                                                                               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 5TPW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (71, 85)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

5tpz 5tq0 5tq2