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(-) Description

Title :  CRYSTAL STRUCTURE OF 2ND PDZ DOMAIN OF GLUTAMATE RECEPTOR INTERACTING PROTEIN-1 (GRIP1)
 
Authors :  J. Tickle, J. Elkins, A. C. W. Pike, C. Cooper, E. Salah, E. Papagrigorio F. Von Delft, A. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom,
Date :  28 Jun 07  (Deposition) - 10 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Endoplasmic Reticulum, Postsynaptic Membrane, Membrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Tickle, J. Elkins, A. C. W. Pike, C. Cooper, E. Salah, E. Papagrigoriou, F. Von Delft, A. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, D. Doyle
Crystal Structure Of 2Nd Pdz Domain Of Glutamate Receptor Interacting Protein-1 (Grip1)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR INTERACTING PROTEIN-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    FragmentPDZ DOMAIN 2, RESIDUES 149-239
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGRIP1 PROTEIN

 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, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2SCN2Ligand/IonTHIOCYANATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2SCN2Ligand/IonTHIOCYANATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2SCN-1Ligand/IonTHIOCYANATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:167 , GLY A:168 , TYR B:236 , SER B:239BINDING SITE FOR RESIDUE SCN A1244
2AC2SOFTWARETYR A:236 , SER A:239 , ARG B:167 , GLY B:168BINDING SITE FOR RESIDUE SCN A1245
3AC3SOFTWARETHR A:150 , VAL A:151 , VAL A:238 , GLU A:240 , ARG B:167 , THR B:183BINDING SITE FOR RESIDUE EDO A1246
4AC4SOFTWAREMET B:0 , ARG B:149 , THR B:150 , GLU B:235BINDING SITE FOR RESIDUE EDO B1244
5AC5SOFTWAREARG A:210 , LEU A:212 , GLY B:163 , PHE B:164 , VAL B:165 , SER B:184 , ARG B:186 , HOH B:2078BINDING SITE FOR RESIDUE EDO B1245

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRIP1_HUMAN53-136
150-238
 
252-336
472-547
573-658
673-755
1004-1086
  2-
A:150-238
B:150-238
-
-
-
-
-
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRIP1_HUMAN53-136
150-238
 
252-336
472-547
573-658
673-755
1004-1086
  1-
A:150-238
-
-
-
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.GRIP1_HUMAN53-136
150-238
 
252-336
472-547
573-658
673-755
1004-1086
  1-
-
B:150-238
-
-
-
-
-

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003597421ENSE00001408638chr12:67072925-67072630296GRIP1_HUMAN1-19190--
1.2ENST000003597422ENSE00001411244chr12:66990707-6699062781GRIP1_HUMAN19-46280--
1.3ENST000003597423ENSE00001417861chr12:66935730-66935595136GRIP1_HUMAN46-91460--
1.4ENST000003597424ENSE00001422180chr12:66933003-66932858146GRIP1_HUMAN91-140500--
1.5ENST000003597425ENSE00001428140chr12:66923694-6692361184GRIP1_HUMAN140-168292A:-1-168 (gaps)
B:-1-168 (gaps)
25
25
1.6ENST000003597426ENSE00001431116chr12:66911756-6691168176GRIP1_HUMAN168-193262A:168-193 (gaps)
B:168-193
26
26
1.7ENST000003597427ENSE00001430548chr12:66909544-66909399146GRIP1_HUMAN193-242502A:193-239
B:193-239
47
47
1.8ENST000003597428ENSE00001023693chr12:66859202-66859055148GRIP1_HUMAN242-291502A:240-243
B:240-243
4
4
1.9ENST000003597429ENSE00001023700chr12:66856873-66856704170GRIP1_HUMAN291-348580--
1.10ENST0000035974210ENSE00001308160chr12:66850122-66849967156GRIP1_HUMAN348-400530--
1.11ENST0000035974211ENSE00001023694chr12:66849344-66849189156GRIP1_HUMAN400-452530--
1.12ENST0000035974212ENSE00001023701chr12:66839288-66839102187GRIP1_HUMAN452-514630--
1.13ENST0000035974213ENSE00001023699chr12:66838509-66838364146GRIP1_HUMAN514-563500--
1.14ENST0000035974214ENSE00001303738chr12:66826408-6682632881GRIP1_HUMAN563-590280--
1.15ENST0000035974215ENSE00001323901chr12:66814569-6681450070GRIP1_HUMAN590-613240--
1.16ENST0000035974216ENSE00001295130chr12:66800208-66800063146GRIP1_HUMAN613-662500--
1.17ENST0000035974217ENSE00001320083chr12:66788132-66787988145GRIP1_HUMAN662-710490--
1.18ENST0000035974218ENSE00001302238chr12:66786596-66786457140GRIP1_HUMAN710-757480--
1.19ENST0000035974219ENSE00001323780chr12:66786282-66786088195GRIP1_HUMAN757-822660--
1.20ENST0000035974220ENSE00001294211chr12:66773216-66773060157GRIP1_HUMAN822-874530--
1.21ENST0000035974221ENSE00001309883chr12:66771065-66770954112GRIP1_HUMAN874-911380--
1.22ENST0000035974222ENSE00001431604chr12:66770841-6677079745GRIP1_HUMAN912-926150--
1.23ENST0000035974223ENSE00001326760chr12:66765707-66765474234GRIP1_HUMAN927-1004780--
1.24ENST0000035974224ENSE00001294875chr12:66747343-66747197147GRIP1_HUMAN1005-1053490--
1.25ENST0000035974225ENSE00001429206chr12:66743026-667412231804GRIP1_HUMAN1054-1128750--

(-) 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:95
 aligned with GRIP1_HUMAN | Q9Y3R0 from UniProtKB/Swiss-Prot  Length:1128

    Alignment length:105
                                   153       163       173       183       193       203       213       223       233       243     
          GRIP1_HUMAN   144 SSVIFRTVEVTLHKEGNTFGFVIRGGAHDDRNKSRPVVITCVRPGGPADREGTIKPGDRLLSVDGIRLLGTTHAEAMSILKQCGQEAALLIEYDVSVMDSVATAS 248
               SCOP domains d   2jila_ A: automated matches                                                                           SCOP domains
               CATH domains 2   jilA00 A:-1-243  [code=2.30  .42.10, no name defined]                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---eeeeeeeee.......eeeeee.....--.eeeeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeeeee..-----.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PDZ  PDB: A:150-238 UniProt: 150-238                                                     ---------- PROSITE
           Transcript 1 (1) Exon 1.5 UniProt: 140-168------------------------Exon 1.7  PDB: A:193-239 UniProt: 193-242         ------ Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.6 UniProt: 168-193 ------------------------------------------------1.8     Transcript 1 (2)
                 2jil A  -1 S---MRTVEVTLHKEGNTFGFVIRGGAHDDR--SRPVVITSVRPGGPADREGTIKPGDRLLSVDGIRLLGTTHAEAMSILKQCGQEAALLIEYDVS-----ETAV 243
                            |   || 153       163       173|  |   183       193       203       213       223       233     |   - |   
                            |   0|                      174  |                                                           239   240   
                           -1  149                         177                                                                       

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with GRIP1_HUMAN | Q9Y3R0 from UniProtKB/Swiss-Prot  Length:1128

    Alignment length:105
                                   153       163       173       183       193       203       213       223       233       243     
          GRIP1_HUMAN   144 SSVIFRTVEVTLHKEGNTFGFVIRGGAHDDRNKSRPVVITCVRPGGPADREGTIKPGDRLLSVDGIRLLGTTHAEAMSILKQCGQEAALLIEYDVSVMDSVATAS 248
               SCOP domains d   2jilb_ B: automated matches                                                                           SCOP domains
               CATH domains 2   jilB00 B:-1-243  [code=2.30.42.10, no name defined]                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---eeeeeeeee.......eeeeee...hhhhheeeeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeeeee..-----eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PDZ  PDB: B:150-238 UniProt: 150-238                                                     ---------- PROSITE
           Transcript 1 (1) Exon 1.5 UniProt: 140-168------------------------Exon 1.7  PDB: B:193-239 UniProt: 193-242         ------ Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.6  PDB: B:168-193  ------------------------------------------------1.8     Transcript 1 (2)
                 2jil B  -1 S---MRTVEVTLHKEGNTFGFVIRGGAHDDRNKSRPVVITSVRPGGPADREGTIKPGDRLLSVDGIRLLGTTHAEAMSILKQCGQEAALLIEYDVS-----ETAV 243
                            |   || 153       163       173       183       193       203       213       223       233     |   - |   
                           -1   0|                                                                                       239   240   
                               149                                                                                                   

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2JIL)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GRIP1_HUMAN | Q9Y3R0)
molecular function
    GO:0050681    androgen receptor binding    Interacting selectively and non-covalently with an androgen receptor.
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0035259    glucocorticoid receptor binding    Interacting selectively and non-covalently with a glucocorticoid receptor.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0030159    receptor signaling complex scaffold activity    Functions to provide a physical support for the assembly of a multiprotein receptor signaling complex.
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
biological process
    GO:0030521    androgen receptor signaling pathway    Any series of molecular signals generated as a consequence of an androgen binding to its receptor.
    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:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
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:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma 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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