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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT GLUTAMATE RECEPTOR DELTA-2 EXTRACELLULAR DOMAIN
 
Authors :  S. Cheng, E. Ozkan
Date :  01 Aug 16  (Deposition) - 28 Dec 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.15
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Synapse Protein, Cell Surface Protein, Glycoprotein, Nervous System, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Cheng, A. B. Seven, J. Wang, G. Skiniotis, E. Ozkan
Conformational Plasticity In The Transsynaptic Neurexin-Cerebellin-Glutamate Receptor Adhesion Complex.
Structure V. 24 2163 2016
PubMed-ID: 27926833  |  Reference-DOI: 10.1016/J.STR.2016.11.004

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, DELTA-2,GLUTAMATE RECEPTOR IONOTROPIC, DELTA-2
    Chains: A, B, C
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE (BTI-TN-5B1-4)
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: GRID2
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUR DELTA-2 SUBUNIT,GLUR DELTA-2 SUBUNIT

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5L2E)

(-) Sites  (0, 0)

(no "Site" information available for 5L2E)

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:83 -A:355
2A:99 -A:131
3A:298 -A:310
4A:756 -A:811
5B:83 -B:355
6B:99 -B:131
7B:298 -B:310
8B:756 -B:811
9C:83 -C:355
10C:99 -C:131
11C:298 -C:310
12C:756 -C:811

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:451 -Pro A:452
2Glu B:451 -Pro B:452
3Glu C:451 -Pro C:452

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L2E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L2E)

(-) Exons   (0, 0)

(no "Exon" information available for 5L2E)

(-) 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:648
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee..hhhhhhhhhhhhhhhhhh........eeeeeeee...hhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhh..eeeee.hhhhh................eee.....hhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeeeeee.......hhhh.ee..ee.hhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh.eee....eee...........eeeee...eeeeeee...eee.....eeeeee.......eeee.......eeehhhhhhhhhhhhhhh.eeeeee...............hhhhhhhhh....eee.....hhhhhhheee....ee..eeeeee....hhhhhh......ee....hhhhhhhhhhhhh..hhhhhhhhhh......hhhhhhhhh...eeeeehhhhhhhhhh.....eeee.......ee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5l2e A  24 DSIIHIGAIFDESAKKDDEVFRTAVGDLNQNEEILQTEKITFSVTFVDGNNPFQAVQEACELMNQGILALVSSIGCTSAGSLQSLADAMHIPHLFIQRSTAGTPRSGCGLTRSNRNDDYTLSVRPPVYLNEVILRVVTEYAWQKFIIFYDSEYDIRGIQEFLDKVSQQGMDVALQKVENNINKMITTLFDTMRIEELNRYRDTLRRAILVMNPATAKSFISEVVETNLVAFDCHWIIINEEINDVDVQELVRRSIGRLTIIRQTFPVPQNISQRCFRGNHRISSTLCDPKDPFAQNMEISNLYIYDTVLLLANAFHKKLQDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGVNGLTGDLEFGENGGNPNVHFEILGTGVRKLGCWNPVTGLNGSLGVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRRSIQSLQDLSKQTDIPYGTVLDSAVYQHVRMKGLNPSMYSQMWRMINNNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQSGDMDILKHKWWPKNGQC 811
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403|      421       441       451       461       471       481       491       501       511       521       531       541       551|      673       683       693    || 707     ||723       733       743       753       763       773       783       793       803        
                                                                                                                                                                                                                                                                                                                                                                                                                     403|              429|                                                                                                            551|                               698|       713|                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                      412               440                                                                                                             664                                703        720                                                                                           


Chain B from PDB  Type:PROTEIN  Length:648
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee..hhhhhhhhhhhhhhhhhh........eeeeeeee...hhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhh..eeeee.hhhhh................eee.....hhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeeeeee.......hhhh.ee..ee.hhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh.eee....eee...........eeeee...eeeeeee...eee.....eeeeee.......eeee.......eeehhhhhhhhhhhhhhh.eeeeee...............hhhhhhhhh....eeeeeee.hhhhhhheee....eee.eeeeee....hhhhhh......ee....hhhhhhhhhhhhh..hhhhhhhhhh......hhhhhhhhh...eeeeehhhhhhhhhh.....eeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5l2e B  24 DSIIHIGAIFDESAKKDDEVFRTAVGDLNQNEEILQTEKITFSVTFVDGNNPFQAVQEACELMNQGILALVSSIGCTSAGSLQSLADAMHIPHLFIQRSTAGTPRSGCGLTRSNRNDDYTLSVRPPVYLNEVILRVVTEYAWQKFIIFYDSEYDIRGIQEFLDKVSQQGMDVALQKVENNINKMITTLFDTMRIEELNRYRDTLRRAILVMNPATAKSFISEVVETNLVAFDCHWIIINEEINDVDVQELVRRSIGRLTIIRQTFPVPQNISQRCFRGNHRISSTLCDPKDPFAQNMEISNLYIYDTVLLLANAFHKKLQDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGVNGLTGDLEFGENGGNPNVHFEILGTGVRKLGCWNPVTGLNGSLGVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRRSIQSLQDLSKQTDIPYGTVLDSAVYQHVRMKGLNPSMYSQMWRMINNNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQSGDMDILKHKWWPKNGQC 811
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403|      421       441       451       461       471       481       491       501       511       521       531       541       551|      673       683       693    || 707     ||723       733       743       753       763       773       783       793       803        
                                                                                                                                                                                                                                                                                                                                                                                                                     403|              429|                                                                                                            551|                               698|       713|                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                      412               440                                                                                                             664                                703        720                                                                                           


Chain C from PDB  Type:PROTEIN  Length:648
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee..hhhhhhhhhhhhhhhhhh........eeeeeeee...hhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhh..eeeee.hhhhh................eee.....hhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeeeeee.......hhhh.ee..ee.hhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh.eeee..eeee...........eeeee...eeeeeee...eee.....eeeeee.......eeee.......eeehhhhhhhhhhhhhhh.eeeeee...............hhhhhhhhh....eee.....hhhhhhheee....eee.eeeeee....hhhhhh......ee....hhhhhhhhhhhhh..hhhhhhhhhh......hhhhhhhhh...eeeeehhhhhhhhhh.....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5l2e C  24 DSIIHIGAIFDESAKKDDEVFRTAVGDLNQNEEILQTEKITFSVTFVDGNNPFQAVQEACELMNQGILALVSSIGCTSAGSLQSLADAMHIPHLFIQRSTAGTPRSGCGLTRSNRNDDYTLSVRPPVYLNEVILRVVTEYAWQKFIIFYDSEYDIRGIQEFLDKVSQQGMDVALQKVENNINKMITTLFDTMRIEELNRYRDTLRRAILVMNPATAKSFISEVVETNLVAFDCHWIIINEEINDVDVQELVRRSIGRLTIIRQTFPVPQNISQRCFRGNHRISSTLCDPKDPFAQNMEISNLYIYDTVLLLANAFHKKLQDRKWHSMASLSCIRKNSKPWQGGRSMLETIKKGGVNGLTGDLEFGENGGNPNVHFEILGTGVRKLGCWNPVTGLNGSLGVVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRRSIQSLQDLSKQTDIPYGTVLDSAVYQHVRMKGLNPSMYSQMWRMINNNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQSGDMDILKHKWWPKNGQC 811
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403|      421       441       451       461       471       481       491       501       511       521       531       541       551|      673       683       693    || 707     ||723       733       743       753       763       773       783       793       803        
                                                                                                                                                                                                                                                                                                                                                                                                                     403|              429|                                                                                                            551|                               698|       713|                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                      412               440                                                                                                             664                                703        720
   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 5L2E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L2E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L2E)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)

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  Sites
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  Cis Peptide Bonds
    Glu A:451 - Pro A:452   [ RasMol ]  
    Glu B:451 - Pro B:452   [ RasMol ]  
    Glu C:451 - Pro C:452   [ RasMol ]  
 
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  5l2e
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 Related Entries

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

UniProtKB/Swiss-Prot
        GRID2_RAT | Q63226: 2v3t 2v3u 5cc2

(-) Related Entries Specified in the PDB File

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