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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NR3A LIGAND BINDING CORE COMPLEX WITH D-SERINE AT 1.45 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 :  1.45
Chains :  Asym./Biol. Unit :  A,B
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 3A
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B(+) MODIFIED
    Expression System StrainORIGAMIB (DE3)
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 511-660, 776-915
    GeneGRIN3A
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Other DetailsPEPTIDES CORRESPONDING TO N511-R660 AND E776-K915 WERE COUPLED BY A GT DIPEPTIDE SYNTHETIC LINKER
    SynonymN-METHYL-D-ASPARTATE RECEPTOR SUBTYPE 3A, NR3A, NMDAR-L, NMDAR-L1, N-METHYL-D-ASPARTATE RECEPTOR, CHI-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2DSN2Ligand/IonD-SERINE
3GOL3Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:21 , ALA A:31 , CYS A:67 , HOH A:1143 , HOH A:1210BINDING SITE FOR RESIDUE CL A 296
2AC2SOFTWARETYR A:97 , SER A:123 , SER A:125 , ARG A:130 , SER A:179 , SER A:180 , ALA A:181 , MET A:223 , ASP A:224 , TYR A:252BINDING SITE FOR RESIDUE DSN A 901
3AC3SOFTWARETYR B:97 , SER B:123 , PHE B:124 , SER B:125 , ARG B:130 , SER B:179 , SER B:180 , ALA B:181 , MET B:223 , ASP B:224 , TYR B:252BINDING SITE FOR RESIDUE DSN A 902
4AC4SOFTWAREPRO A:258 , ASN A:259 , HOH A:992 , PRO B:258 , HOH B:369 , HOH B:516BINDING SITE FOR RESIDUE GOL B 296
5AC5SOFTWAREASP A:74 , LYS A:285 , HOH A:943 , HOH A:991 , HOH A:1154 , ASP B:214 , PRO B:215BINDING SITE FOR RESIDUE GOL A 903
6AC6SOFTWAREGLY A:115 , PRO A:258 , HOH A:1010 , HOH A:1070 , PRO B:258 , ASN B:259 , HOH B:609BINDING SITE FOR RESIDUE GOL A 904

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:29 -A:67
2A:35 -A:68
3B:29 -B:67
4B:35 -B:68

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1His A:15 -Pro A:16
2Asp A:214 -Pro A:215
3His B:15 -Pro B:16
4Asp B:214 -Pro B:215

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RC8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RC8)

(-) Exons   (0, 0)

(no "Exon" information available for 2RC8)

(-) 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:284
 aligned with NMD3A_RAT | Q9R1M7 from UniProtKB/Swiss-Prot  Length:1135

    Alignment length:397
                                   521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       
            NMD3A_RAT   512 KLHLRVVTLIEHPFVFTREVDDEGLCPAGQLCLDPMTNDSSMLDRLFSSLHSSNDTVPIKFKKCCYGYCIDLLEQLAEDMNFDFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDTAAPIGAFMWPLHWTMWLGIFVALHITAIFLTLYEWKSPFGMTPKGRNRNKVFSFSSALNVCYALLFGRTAAIKPPKCWTGRFLMNLWAIFCMFCLSTYTANLAAVMVGEKIYEELSGIHDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQYLKNDPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWY 908
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eee...........eeee.....hhhhhhhhhhhhhh.....hhh.eeeeehhhhhhhhhhhhhhheeeeeee........ee..eehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee....-----------------------------------------------------------------------------------------------------------------......hhhhhh......ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh......eeeeehhhhhhhhhh.....eee....eeeeee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rc8 A   4 KLHLRVVTLIEHPFVFTREVDDEGLCPAGQLCLDPMTNDSSMLDRLFSSLHSSNDTVPIKFKKCCYGYCIDLLEQLAEDMNFDFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRGT-----------------------------------------------------------------------------------------------------------------ELSGIHDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQYLKNDPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWY 287
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153|        -         -         -         -         -         -         -         -         -         -         -    |  160       170       180       190       200       210       220       230       240       250       260       270       280       
                                                                                                                                                                                154                                                                                                               155                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:285
 aligned with NMD3A_RAT | Q9R1M7 from UniProtKB/Swiss-Prot  Length:1135

    Alignment length:398
                                   521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901        
            NMD3A_RAT   512 KLHLRVVTLIEHPFVFTREVDDEGLCPAGQLCLDPMTNDSSMLDRLFSSLHSSNDTVPIKFKKCCYGYCIDLLEQLAEDMNFDFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRDTAAPIGAFMWPLHWTMWLGIFVALHITAIFLTLYEWKSPFGMTPKGRNRNKVFSFSSALNVCYALLFGRTAAIKPPKCWTGRFLMNLWAIFCMFCLSTYTANLAAVMVGEKIYEELSGIHDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQYLKNDPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWYK 909
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Lig_chan-2rc8B01 B:155-288                                                                                                             Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Lig_chan-2rc8B02 B:155-288                                                                                                             Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------SBP_bac_3-2rc8B03 B:55-288                                                                          -----------------------------------------------------------------------------------------------------------------                                                                                                                                       Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------SBP_bac_3-2rc8B04 B:55-288                                                                          -----------------------------------------------------------------------------------------------------------------                                                                                                                                       Pfam domains (4)
         Sec.struct. author .eeeeeee.......eeee..........eeee.....hhhhhhhhhhhhh......hhh.eeeeehhhhhhhhhhhhhh.eeeeeee........ee..eehhhhhhhhh....ee......hhhhhh..ee....eeeeeeeeee....-----------------------------------------------------------------------------------------------------------------......hhhhhhhhhh..ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh......eeeeehhhhhhhhhh.....eee....eeeeee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rc8 B   4 KLHLRVVTLIEHPFVFTREVDDEGLCPAGQLCLDPMTNDSSMLDRLFSSLHSSNDTVPIKFKKCCYGYCIDLLEQLAEDMNFDFDLYIVGDGKYGAWKNGHWTGLVGDLLSGTANMAVTSFSINTARSQVIDFTSPFFSTSLGILVRTRGT-----------------------------------------------------------------------------------------------------------------ELSGIHDPKLHHPSQGFRFGTVRESSAEDYVRQSFPEMHEYMRRYNVPATPDGVQYLKNDPEKLDAFIMDKALLDYEVSIDADCKLLTVGKPFAIEGYGIGLPPNSPLTSNISELISQYKSHGFMDVLHDKWYK 288
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153|        -         -         -         -         -         -         -         -         -         -         -    |  160       170       180       190       200       210       220       230       240       250       260       270       280        
                                                                                                                                                                                154                                                                                                               155                                                                                                                                     

   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 2RC8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RC8)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NMD3A_RAT | Q9R1M7)
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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0051721    protein phosphatase 2A binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 2A.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0006816    calcium ion transport    The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    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
        NMD3A_RAT | Q9R1M72rc7 2rc9 4kcd

(-) Related Entries Specified in the PDB File

1pb7 NR1 COMPLEX WITH GLYCINE
1pb8 NR1 COMPLEX WITH D-SERINE
2rc7 NR3A COMPLEX WITH GLYCINE
2rc9 NR3A COMPLEX WITH ACPC
2rca NR3B COMPLEX WITH GLYCINE
2rcb NR3B COMPLEX WITH D-SERINE