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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NR3B LIGAND BINDING CORE COMPLEX WITH GLYCINE AT 1.58 ANGSTROM RESOLUTION
 
Authors :  Y. Yao, M. L. Mayer
Date :  19 Sep 07  (Deposition) - 05 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Membrane Protein, Cell Junction, Glycoprotein, Ion Transport, Ionic Channel, Magnesium, Postsynaptic Cell Membrane, Receptor, Synapse, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Yao, C. B. Harrison, P. L. Freddolino, K. Schulten, M. L. Mayer
Molecular Mechanism Of Ligand Recognition By Nr3 Subtype Glutamate Receptors.
Embo J. V. 27 2158 2008
PubMed-ID: 18636091  |  Reference-DOI: 10.1038/EMBOJ.2008.140
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE [NMDA] RECEPTOR SUBUNIT 3B
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B(+) MODIFIED
    Expression System StrainORIGAMIB (DE3)
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 413-560, 676-815
    GeneGRIN3B
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Other DetailsPEPTIDES CORRESPONDING TO A413-R560 AND E676-K815 WERE COUPLED BY A GT DIPEPTIDE SYNTHETIC LINKER
    SynonymN-METHYL-D-ASPARTATE RECEPTOR SUBTYPE 3B, NR3B, NMDAR3B

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GLY-1Mod. Amino AcidGLYCINE
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:95 , SER A:121 , SER A:123 , ARG A:128 , SER A:177 , SER A:178 , ASP A:222BINDING SITE FOR RESIDUE GLY A 901
2AC2SOFTWARETYR B:95 , SER B:121 , SER B:123 , ARG B:128 , SER B:177 , SER B:178 , ASP B:222BINDING SITE FOR RESIDUE GLY A 902
3AC3SOFTWAREGLY A:113 , HIS A:116 , HOH A:1114 , HOH A:1181BINDING SITE FOR RESIDUE GOL A 903

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:29 -A:65
2A:35 -A:66
3B:29 -B:65
4B:35 -B:66

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1His A:15 -Pro A:16
2Asp A:212 -Pro A:213
3His B:15 -Pro B:16
4Val B:54 -Asn B:55
5Asp B:212 -Pro B:213

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RCA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RCA)

(-) Exons   (0, 0)

(no "Exon" information available for 2RCA)

(-) 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:284
 aligned with NMD3B_RAT | Q8VHN2 from UniProtKB/Swiss-Prot  Length:1002

    Alignment length:402
                                   423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813  
            NMD3B_RAT   414 RPKLRVVTLVEHPFVFTRESDEDGQCPAGQLCLDPGTNDSARLDALFAALVNGSVPRTLRRCCYGYCIDLLERLAEDLAFDFELYIVGDGKYGALRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRTRDTASPIGAFMWPLHWSMWVGVFAALHLTALFLTLYEWRSPYGLTPRGRNRGTVFSYSSALNLCYAILFGRTVSSKTPKCPTGRFLMNLWAIFCLLVLSSYTANLAAVMVGDKTFEELSGIHDPKLHHPSQGFRFGTVWESSAEAYIKASFPEMHAHMRRHSAPTTPHGVAMLTSDPPKLNAFIMDKSLLDYEVSIDADCKLLTVGKPFAIEGYGIGLPQNSPLTSNLSEFISRYKSSGFIDLLHDKWYKMVPCGK 815
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.......eeee..........eeee.....hhhhhhhhhhhhhhh..hhh.eeeeehhhhhhhhhhhhhhh.eeeeee........ee..eehhhhhhhhh....ee......hhhhhh.eee....eeeeeeeeee.--------------------------------------------------...---------------------------------------------------------------......hhhhhh......ee....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh......eeeeehhhhhhhhhhh....eeeeeeeeeeeee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh-----.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rca A   4 RPKLRVVTLVEHPFVFTRESDEDGQCPAGQLCLDPGTNDSARLDALFAALVNGSVPRTLRRCCYGYCIDLLERLAEDLAFDFELYIVGDGKYGALRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRT--------------------------------------------------RGT---------------------------------------------------------------ELSGIHDPKLHHPSQGFRFGTVWESSAEAYIKASFPEMHAHMRRHSAPTTPHGVAMLTSDPPKLNAFIMDKSLLDYEVSIDADCKLLTVGKPFAIEGYGIGLPQNSPLTSNLSEFISRYKSSGFIDLLHDKWY-----GG 902
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     |   -         -         -         -         -      | |-         -         -         -         -         -         -  |    160       170       180       190       200       210       220       230       240       250       260       270       280    |    -| 
                                                                                                                                                                           149                                                150 |                                                             153                                                                                                                                 285   901 
                                                                                                                                                                                                                                152                                                                                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with NMD3B_RAT | Q8VHN2 from UniProtKB/Swiss-Prot  Length:1002

    Alignment length:395
                                   423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803     
            NMD3B_RAT   414 RPKLRVVTLVEHPFVFTRESDEDGQCPAGQLCLDPGTNDSARLDALFAALVNGSVPRTLRRCCYGYCIDLLERLAEDLAFDFELYIVGDGKYGALRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRTRDTASPIGAFMWPLHWSMWVGVFAALHLTALFLTLYEWRSPYGLTPRGRNRGTVFSYSSALNLCYAILFGRTVSSKTPKCPTGRFLMNLWAIFCLLVLSSYTANLAAVMVGDKTFEELSGIHDPKLHHPSQGFRFGTVWESSAEAYIKASFPEMHAHMRRHSAPTTPHGVAMLTSDPPKLNAFIMDKSLLDYEVSIDADCKLLTVGKPFAIEGYGIGLPQNSPLTSNLSEFISRYKSSGFIDLLHDKWY 808
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Lig_chan-2rcaB01 B:153-285                                                                                                            Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Lig_chan-2rcaB02 B:153-285                                                                                                            Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------SBP_bac_3-2rcaB03 B:66-285                                                          --------------------------------------------------   ---------------------------------------------------------------                                                                                                                                      Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------SBP_bac_3-2rcaB04 B:66-285                                                          --------------------------------------------------   ---------------------------------------------------------------                                                                                                                                      Pfam domains (4)
         Sec.struct. author ..eeeeee.......eee...........eeee.....hhhhhhhhhhhhh....hhh.eeeeehhhhhhhhhhhhhh..eeeeee........ee..eehhhhhhhhh....ee......hhhhhh.eee....eeeeeeeeee.--------------------------------------------------...---------------------------------------------------------------......hhhhhh......ee....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh......eeeeehhhhhhhhhhh....eeeeeeeeeeeee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rca B   4 RPKLRVVTLVEHPFVFTRESDEDGQCPAGQLCLDPGTNDSARLDALFAALVNGSVPRTLRRCCYGYCIDLLERLAEDLAFDFELYIVGDGKYGALRDGRWTGLVGDLLAGRAHMAVTSFSINSARSQVVDFTSPFFSTSLGIMVRT--------------------------------------------------RGT---------------------------------------------------------------ELSGIHDPKLHHPSQGFRFGTVWESSAEAYIKASFPEMHAHMRRHSAPTTPHGVAMLTSDPPKLNAFIMDKSLLDYEVSIDADCKLLTVGKPFAIEGYGIGLPQNSPLTSNLSEFISRYKSSGFIDLLHDKWY 285
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     |   -         -         -         -         -      | |-         -         -         -         -         -         -  |    160       170       180       190       200       210       220       230       240       250       260       270       280     
                                                                                                                                                                           149                                                150 |                                                             153                                                                                                                                    
                                                                                                                                                                                                                                152                                                                                                                                                                                                    

   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 2RCA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RCA)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NMD3B_RAT | Q8VHN2)
molecular function
    GO:0004972    NMDA glutamate receptor activity    An cation channel that opens in response to binding by extracellular glutmate, but only if glycine is also bound and the membrane is depolarized. Voltage gating is indirect, due to ejection of bound magnesium from the pore at permissive voltages.
    GO:0005261    cation channel activity    Enables the energy-independent passage of cations across a lipid bilayer down a concentration gradient.
    GO:0005234    extracellular-glutamate-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when extracellular glutamate has been bound by the channel complex or one of its constituent parts.
    GO:0016594    glycine binding    Interacting selectively and non-covalently with glycine, aminoethanoic acid.
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    GO:0004970    ionotropic glutamate receptor activity    Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts.
    GO:0042165    neurotransmitter binding    Interacting selectively and non-covalently with a neurotransmitter, any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.
    GO:0030594    neurotransmitter receptor activity    Combining with a neurotransmitter and transmitting the signal to initiate a change in cell activity.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0098655    cation transmembrane transport    A process in which a cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0099565    chemical synaptic transmission, postsynaptic    The part of synaptic transmission occurring in the post-synapse: a signal transduction pathway consisting of neurotransmitter receptor activation and its effects on postsynaptic membrane potential and the ionic composition of the postsynaptic cytosol.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0035235    ionotropic glutamate receptor signaling pathway    A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0017146    NMDA selective glutamate receptor complex    An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. NMDA receptors are composed of assemblies of NR1 subunits (Figure 3) and NR2 subunits, which can be one of four separate gene products (NR2A-D). Expression of both subunits are required to form functional channels. The glutamate binding domain is formed at the junction of NR1 and NR2 subunits. NMDA receptors are permeable to calcium ions as well as being permeable to other ions. Thus NMDA receptor activation leads to a calcium influx into the post-synaptic cells, a signal thought to be crucial for the induction of NMDA-receptor dependent LTP and LTD.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NMD3B_RAT | Q8VHN22rcb

(-) Related Entries Specified in the PDB File

1pb7 NR1 COMPLEX WITH GLYCINE
2rc7 NR3A COMPLEX WITH GLYCINE
2rc8 NR3A COMPLEX WITH D-SERINE
2rc9 NR3A COMPLEX WITH ACPC
2rcb NR3B COMPLEX WITH D-SERINE