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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUN2D LIGAND-BINDING CORE IN COMPLEX WITH L-GLUTAMATE
 
Authors :  N. Simorowski, H. Furukawa
Date :  12 Aug 10  (Deposition) - 11 May 11  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Ion Channel, L-Glutamate, Disulfide Bonds, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. M. Vance, N. Simorowski, S. F. Traynelis, H. Furukawa
Ligand-Specific Deactivation Time Course Of Glun1/Glun2D Nmda Receptors.
Nat Commun V. 2 294 2011
PubMed-ID: 21522138  |  Reference-DOI: 10.1038/NCOMMS1295

(-) Compounds

Molecule 1 - GLUTAMATE [NMDA] RECEPTOR SUBUNIT EPSILON-4
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainORIGAMIB(DE3)
    Expression System Taxid562
    FragmentUNP RESIDUES 424-564, 686-827
    GeneGLUN2D, GRIN2D
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymN-METHYL D-ASPARTATE RECEPTOR SUBTYPE 2D, NMDAR2D, NR2D

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GLU1Mod. Amino AcidGLUTAMIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:88 , SER A:114 , THR A:116 , ARG A:121 , GLY A:172 , SER A:173 , THR A:174 , TYR A:214 , ASP A:215 , HOH A:316 , HOH A:321BINDING SITE FOR RESIDUE GLU A 1001

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:30 -A:58
2A:37 -A:59
3A:229 -A:284

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:15 -Pro A:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OEN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OEN)

(-) Exons   (0, 0)

(no "Exon" information available for 3OEN)

(-) 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:251
 aligned with NMDE4_RAT | Q62645 from UniProtKB/Swiss-Prot  Length:1323

    Alignment length:403
                                   435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825   
           NMDE4_RAT    426 TQHLTVATLEERPFVIVEPADPISGTCIRDSVPCRSQLNRTHSPPPDAPRPEKRCCKGFCIDILKRLAHTIGFSYDLYLVTNGKHGKKIDGVWNGMIGEVFYQRADMAIGSLTINEERSEIVDFSVPFVETGISVMVARSNGTVSPSAFLEPYSPAVWVMMFVMCLTVVAVTVFIFEYLSPVGYNRSLATGKRPGGSTFTIGKSIWLLWALVFNNSVPVENPRGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYVDTVSGLSDRKFQRPQEQYPPLKFGTVPNGSTEKNIRSNYPDMHSYMVRYNQPRVEEALTQLKAGKLDAFIYDAAVLNYMARKDEGCKLVTIGSGKVFATTGYGIALHKGSRWKRPIDLALLQFLGDDEIEMLERLWLSGICHND  828
               SCOP domains d3oena_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Lig_chan-3oenA01 A:163-285                                                                                                 -- Pfam domains (1)
           Pfam domains (2) --------------------------------------            SBP_bac_3-3oenA02 A:54-282                                                                                                                                                                                                                                                                                                                                  --- - Pfam domains (2)
         Sec.struct. author ..eeeeee.......eeee............ee.ee..------------...eeeehhhhhhhhhhhhhhh.eeeeee........ee..eehhhhhhhhh....ee......hhhhhh.eee....eeeeeeeeee.-------------------------------------------------------------------------------------------------------------------------------------------...ee....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eeeeehhhhhhhhhhhhhh.eeehhhhh.eeeeee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh....-. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3oen A    4 TQHLTVATLEERPFVIVEPADPISGTCIRDSVPCRSQL------------PEKRCCKGFCIDILKRLAHTIGFSYDLYLVTNGKHGKKIDGVWNGMIGEVFYQRADMAIGSLTINEERSEIVDFSVPFVETGISVMVAR-------------------------------------------------------------------------------------------------------------------------------------------PLKFGTVPNGSTEKNIRSNYPDMHSYMVRYNQPRVEEALTQLKAGKLDAFIYDAAVLNYMARKDEGCKLVTIGSGKVFATTGYGIALHKGSRWKRPIDLALLQFLGDDEIEMLERLWLSGICH-E 1001
                                    13        23        33       | -         -|       63        73        83        93       103       113       123       133        |-         -         -         -         -         -         -         -         -         -         -         -         -         -       164       174       184       194       204       214       224       234       244       254       264       274       284| |
                                                                41           54                                                                                     142                                                                                                                                         163                                                                                                                       285 |
                                                                                                                                                                                                                                                                                                                                                                                                                                           1001

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OEN)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NMDE4_RAT | Q62645)
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:0016595    glutamate binding    Interacting selectively and non-covalently with glutamate, the anion of 2-aminopentanedioic 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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0022843    voltage-gated cation channel activity    Enables the transmembrane transfer of a cation by a voltage-gated channel. A cation is a positively charged ion. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
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: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:0034765    regulation of ion transmembrane transport    Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
    GO:0035249    synaptic transmission, glutamatergic    The vesicular release of glutamate from a presynapse, across a chemical synapse, the subsequent activation of glutamate 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: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:0008328    ionotropic glutamate receptor complex    A multimeric 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.
    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
        NMDE4_RAT | Q626453oek 3oel 3oem 4jwy

(-) Related Entries Specified in the PDB File

3oek 3oel 3oem