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(-) Description

Title :  CRYSTAL STRUCTURE OF GRIP1 PDZ12 IN COMPLEX WITH THE FRAS1 PEPTIDE
 
Authors :  J. Long, Z. Wei, W. Feng, Y. Zhao, M. Zhang
Date :  01 Aug 07  (Deposition) - 03 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,X,Y
Biol. Unit 1:  A,X  (1x)
Biol. Unit 2:  B,Y  (1x)
Keywords :  Pdz-Peptide Complex, Pdz Tandem, Alternative Splicing, Cell Junction, Cytoplasm, Endoplasmic Reticulum, Membrane, Postsynaptic Cell Membrane, Synapse, Protein Binding, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Long, Z. Wei, W. Feng, C. Yu, Y. X. Zhao, M. Zhang
Supramodular Nature Of Grip1 Revealed By The Structure Of Its Pdz12 Tandem In Complex With The Carboxyl Tail Of Fras1.
J. Mol. Biol. V. 375 1457 2008
PubMed-ID: 18155042  |  Reference-DOI: 10.1016/J.JMB.2007.11.088
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR-INTERACTING PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    FragmentPDZ12
    GeneGRIP1
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    SynonymGRIP1 PROTEIN, AMPA RECEPTOR-INTERACTING PROTEIN GRIP1
 
Molecule 2 - (ASN)(ASN)(LEU)(GLN)(ASP)(GLY)(THR)(GLU)(VAL)
    ChainsX, Y
    EngineeredYES
    Other DetailsCOMMERCIALLY SYNTHESIZED
    SynonymFRAS1
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABXY
Biological Unit 1 (1x)A X 
Biological Unit 2 (1x) B Y

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACY-1Ligand/IonACETIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:93 , PHE A:162 , PHE A:164 , MET A:220 , HOH A:257 , HOH A:312BINDING SITE FOR RESIDUE EDO A 1
2AC2SOFTWAREASP B:93 , THR B:161 , PHE B:162 , PHE B:164 , HOH B:283 , HOH B:285BINDING SITE FOR RESIDUE EDO B 2
3AC3SOFTWARELYS A:49 , ARG A:84BINDING SITE FOR RESIDUE ACY A 244
4AC4SOFTWAREARG A:174 , ARG A:178 , GLU B:152 , GLU B:194 , THR B:196BINDING SITE FOR RESIDUE ACY A 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QT5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QT5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QT5)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRIP1_RAT53-136
 
150-238
 
252-336
471-546
572-657
672-754
988-1070
  4A:53-136
B:53-136
A:150-238
B:150-238
-
-
-
-
-
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRIP1_RAT53-136
 
150-238
 
252-336
471-546
572-657
672-754
988-1070
  2A:53-136
-
A:150-238
-
-
-
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRIP1_RAT53-136
 
150-238
 
252-336
471-546
572-657
672-754
988-1070
  2-
B:53-136
-
B:150-238
-
-
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2QT5)

(-) 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:194
 aligned with GRIP1_RAT | P97879 from UniProtKB/Swiss-Prot  Length:1112

    Alignment length:194
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236    
           GRIP1_RAT     47 EFKGSTVVELMKKEGTTLGLTVSGGIDKDGKPRVSNLRQGGIAARSDQLDVGDYIKAVNGINLAKFRHDEIISLLKNVGERVVLEVEYELPPVSIQGSSVMFRTVEVTLHKEGNTFGFVIRGGAHDDRNKSRPVVITCVRPGGPADREGTIKPGDRLLSVDGIRLLGTTHAEAMSILKQCGQEATLLIEYDVSV  240
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee........eeee.........eeeee...hhhhhh.......eeeee..ee....hhhhhhhhhhh...eeeeeeeee..........eeeeeeeeeee.......eeeeee........eeeeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PDZ  PDB: A:53-136 UniProt: 53-136                                                  -------------PDZ  PDB: A:150-238 UniProt: 150-238                                                     -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qt5 A   47 SFKGSTVVELMKKEGTTLGLTVSGGIDKDGKPRVSNLRQGGIAARSDQLDVGDYIKAVNGINLAKFRHDEIISLLKNVGERVVLEVEYELPPVSIQGSSVMFRTVEVTLHKEGNTFGFVIRGGAHDDRNKSRPVVITCVRPGGPADREGTIKPGDRLLSVDGIRLLGTTHAEAMSILKQCGQEATLLIEYDVSV  240
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236    

Chain B from PDB  Type:PROTEIN  Length:193
 aligned with GRIP1_RAT | P97879 from UniProtKB/Swiss-Prot  Length:1112

    Alignment length:193
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236   
           GRIP1_RAT     47 EFKGSTVVELMKKEGTTLGLTVSGGIDKDGKPRVSNLRQGGIAARSDQLDVGDYIKAVNGINLAKFRHDEIISLLKNVGERVVLEVEYELPPVSIQGSSVMFRTVEVTLHKEGNTFGFVIRGGAHDDRNKSRPVVITCVRPGGPADREGTIKPGDRLLSVDGIRLLGTTHAEAMSILKQCGQEATLLIEYDVS  239
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------PDZ-2qt5B01 B:152-235                                                               ---- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------PDZ-2qt5B02 B:152-235                                                               ---- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------PDZ-2qt5B03 B:152-235                                                               ---- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------PDZ-2qt5B04 B:152-235                                                               ---- Pfam domains (4)
         Sec.struct. author ..eeeeeeeee........eeee.........eeeee...hhhhhh.......eeeee..ee....hhhhhhhhhhhh..eeeeeeeee...........eeeeeeeeee.......eeeee...........eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PDZ  PDB: B:53-136 UniProt: 53-136                                                  -------------PDZ  PDB: B:150-238 UniProt: 150-238                                                     - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qt5 B   47 SFKGSTVVELMKKEGTTLGLTVSGGIDKDGKPRVSNLRQGGIAARSDQLDVGDYIKAVNGINLAKFRHDEIISLLKNVGERVVLEVEYELPPVSIQGSSVMFRTVEVTLHKEGNTFGFVIRGGAHDDRNKSRPVVITCVRPGGPADREGTIKPGDRLLSVDGIRLLGTTHAEAMSILKQCGQEATLLIEYDVS  239
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236   

Chain X from PDB  Type:PROTEIN  Length:4
                                     
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .eee Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                2qt5 X 1006 GTEV 1009

Chain Y from PDB  Type:PROTEIN  Length:4
                                     
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .eee Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                2qt5 Y 2006 GTEV 2009

   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 2QT5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QT5)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)
1aPDZ-2qt5B01B:152-235
1bPDZ-2qt5B02B:152-235
1cPDZ-2qt5B03B:152-235
1dPDZ-2qt5B04B:152-235

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GRIP1_RAT | P97879)
molecular function
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0030159    receptor signaling complex scaffold activity    Functions to provide a physical support for the assembly of a multiprotein receptor signaling complex.
biological process
    GO:0016358    dendrite development    The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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
        GRIP1_RAT | P978791m5z 1n7e 1n7f 1p1d 1p1e

(-) Related Entries Specified in the PDB File

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