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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CARBOXY TERMINUS OF HOMER3
 
Authors :  M. K. Hayashi, M. H. Stearns, V. Giannini, R. -M. Xu, C. Sala, Y. Hayashi
Date :  18 Apr 08  (Deposition) - 31 Mar 09  (Release) - 28 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Coiled Coil, Alternative Splicing, Cell Junction, Cytoplasm, Membrane, Phosphoprotein, Polymorphism, Postsynaptic Cell Membrane, Synapse, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. K. Hayashi, C. Tang, C. Verpelli, R. Narayanan, M. H. Stearns, R. M. Xu, H. Li, C. Sala, Y. Hayashi
The Postsynaptic Density Proteins Homer And Shank Form A Polymeric Network Structure.
Cell(Cambridge, Mass. ) V. 137 159 2009
PubMed-ID: 19345194  |  Reference-DOI: 10.1016/J.CELL.2009.01.050
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOMER PROTEIN HOMOLOG 3
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCOILED-COIL REGION, RESIDUES 287-361
    GeneHOMER3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHOMER-3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (1x)  CD
Biological Unit 3 (1x)AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3CVF)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CVF)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:360 -Pro A:361

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 4)

Asymmetric Unit (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_017410S342RHOME3_HUMANPolymorphism1059240A/B/C/DS342R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_017410S342RHOME3_HUMANPolymorphism1059240A/B/C/DS342R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_017410S342RHOME3_HUMANPolymorphism1059240C/DS342R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_017410S342RHOME3_HUMANPolymorphism1059240A/BS342R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (2, 8)

Asymmetric Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003923511ENSE00001511552chr19:19051983-19051860124HOME3_HUMAN-00--
1.2aENST000003923512aENSE00001511549chr19:19049858-1904977881HOME3_HUMAN1-550--
1.3ENST000003923513ENSE00001182908chr19:19049693-19049537157HOME3_HUMAN5-57530--
1.4ENST000003923514ENSE00001223641chr19:19049293-19049162132HOME3_HUMAN58-101440--
1.5bENST000003923515bENSE00001122610chr19:19045219-19045112108HOME3_HUMAN102-137360--
1.6ENST000003923516ENSE00000690660chr19:19043854-19043733122HOME3_HUMAN138-178410--
1.7ENST000003923517ENSE00000690658chr19:19042941-19042785157HOME3_HUMAN178-230530--
1.8ENST000003923518ENSE00000365684chr19:19042434-19042318117HOME3_HUMAN231-269390--
1.9ENST000003923519ENSE00000365685chr19:19042220-1904213487HOME3_HUMAN270-298294A:292-298
B:292-298
C:287-298
D:290-298
7
7
12
9
1.10aENST0000039235110aENSE00001113523chr19:19040443-19040012432HOME3_HUMAN299-361634A:299-361
B:299-361
C:299-360
D:299-361
63
63
62
63

(-) 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:70
 aligned with HOME3_HUMAN | Q9NSC5 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:70
                                   301       311       321       331       341       351       361
          HOME3_HUMAN   292 ETQQKVQDLETRNAELEHQLRAMERSLEEARAERERARAEVGRAAQLLDVSLFELSELREGLARLAEAAP 361
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------R------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
               Transcript 1 1.9    Exon 1.10a  PDB: A:299-361 UniProt: 299-361                     Transcript 1
                 3cvf A 292 ETQQKVQDLETRNAELEHQLRAmERSLEEARAERERARAEVGRAAQLLDVSLFELSELREGLARLAEAAP 361
                                   301       311  |    321       331       341       351       361
                                                314-MSE                                           

Chain B from PDB  Type:PROTEIN  Length:70
 aligned with HOME3_HUMAN | Q9NSC5 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:70
                                   301       311       321       331       341       351       361
          HOME3_HUMAN   292 ETQQKVQDLETRNAELEHQLRAMERSLEEARAERERARAEVGRAAQLLDVSLFELSELREGLARLAEAAP 361
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------R------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
               Transcript 1 1.9    Exon 1.10a  PDB: B:299-361 UniProt: 299-361                     Transcript 1
                 3cvf B 292 ETQQKVQDLETRNAELEHQLRAmERSLEEARAERERARAEVGRAAQLLDVSLFELSELREGLARLAEAAP 361
                                   301       311  |    321       331       341       351       361
                                                314-MSE                                           

Chain C from PDB  Type:PROTEIN  Length:74
 aligned with HOME3_HUMAN | Q9NSC5 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:74
                                   296       306       316       326       336       346       356    
          HOME3_HUMAN   287 AAEREETQQKVQDLETRNAELEHQLRAMERSLEEARAERERARAEVGRAAQLLDVSLFELSELREGLARLAEAA 360
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------R------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.9    Exon 1.10a  PDB: C:299-360 UniProt: 299-361 [INCOMPLETE]       Transcript 1
                 3cvf C 287 AAEREETQQKVQDLETRNAELEHQLRAmERSLEEARAERERARAEVGRAAQLLDVSLFELSELREGLARLAEAA 360
                                   296       306       316       326       336       346       356    
                                                     314-MSE                                          

Chain D from PDB  Type:PROTEIN  Length:72
 aligned with HOME3_HUMAN | Q9NSC5 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:72
                                   299       309       319       329       339       349       359  
          HOME3_HUMAN   290 REETQQKVQDLETRNAELEHQLRAMERSLEEARAERERARAEVGRAAQLLDVSLFELSELREGLARLAEAAP 361
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------R------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.9 Exon 1.10a  PDB: D:299-361 UniProt: 299-361                     Transcript 1
                 3cvf D 290 REETQQKVQDLETRNAELEHQLRAmERSLEEARAERERARAEVGRAAQLLDVSLFELSELREGLARLAEAAP 361
                                   299       309    |  319       329       339       349       359  
                                                  314-MSE                                           

   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 3CVF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CVF)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (HOME3_HUMAN | Q9NSC5)
molecular function
    GO:0035256    G-protein coupled glutamate receptor binding    Interacting selectively and non-covalently with a G-protein coupled glutamate receptor (a metabotropic glutamate 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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0007216    G-protein coupled glutamate receptor signaling pathway    A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. Ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0006605    protein targeting    The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
cellular component
    GO:0045178    basal part of cell    The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue.
    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:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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
        HOME3_HUMAN | Q9NSC52p8v

(-) Related Entries Specified in the PDB File

3cve CRYSTAL STRUCTURE OF THE CARBOXY TERMINUS OF HOMER1