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(-) Description

Title :  AN INTERTWINED HOMODIMER OF THE PDZ HOMOLOGY DOMAIN OF PERIAXIN
 
Authors :  H. Han, P. Kursula
Date :  20 Jan 14  (Deposition) - 02 Apr 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Cell Cycle, Domain Swapping, Intertwining (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Han, P. Kursula
Periaxin And Ahnak Nucleoprotein 2 Form Intertwined Homodimers Through Domain Swapping
J. Biol. Chem. V. 289 14121 2014
PubMed-ID: 24675079  |  Reference-DOI: 10.1074/JBC.M114.554816

(-) Compounds

Molecule 1 - PERIAXIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector: PETM11
    Expression System Vector Type: PLASMID
    Fragment: PDZ DOMAIN, RESIDUES 14-104
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4CMZ)

(-) Sites  (0, 0)

(no "Site" information available for 4CMZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CMZ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:102 -Gly A:103
2Pro B:101 -Thr B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CMZ)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.PRAX_HUMAN16-85
 
 		  3A:16-85
B:16-85
C:16-85
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.PRAX_HUMAN16-85
 
 		  2A:16-85
B:16-85
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.PRAX_HUMAN16-85
 
 		  2-
-
C:16-85

(-) Exons   (0, 0)

(no "Exon" information available for 4CMZ)

(-) 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:90
 aligned with PRAX_HUMAN | Q9BXM0 from UniProtKB/Swiss-Prot  Length:1461

    Alignment length:90
                                    23        33        43        53        63        73        83        93       103
           PRAX_HUMAN    14 AELVEIIVETEAQTGVSGINVAGGGKEGIFVRELREDSPAARSLSLQEGDQLLSARVFFENFKYEDALRLLQCAEPYKVSFCLKRTVPTG 103
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee...ee....eeeeee...eeeeeee...hhhhhhh......eeeeeeee....hhhhhhhhhhhhh..eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --PDZ  PDB: A:16-85 UniProt: 16-85                                      ------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4cmz A  14 AELVEIIVETEAQTGVSGINVAGGGKEGIFVRELREDSPAARSLSLQEGDQLLSARVFFENFKYEDALRLLQCAEPYKVSFCLKRTVPTG 103
                                    23        33        43        53        63        73        83        93       103


Chain B from PDB  Type:PROTEIN  Length:91
 aligned with PRAX_HUMAN | Q9BXM0 from UniProtKB/Swiss-Prot  Length:1461

    Alignment length:91
                                    23        33        43        53        63        73        83        93       103 
           PRAX_HUMAN    14 AELVEIIVETEAQTGVSGINVAGGGKEGIFVRELREDSPAARSLSLQEGDQLLSARVFFENFKYEDALRLLQCAEPYKVSFCLKRTVPTGD 104
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...ee......eeeehhheeee......hhhhhh.......eeeeeeee....hhhhhhhhhhhhh..eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --PDZ  PDB: B:16-85 UniProt: 16-85                                      ------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4cmz B  14 AELVEIIVETEAQTGVSGINVAGGGKEGIFVRELREDSPAARSLSLQEGDQLLSARVFFENFKYEDALRLLQCAEPYKVSFCLKRTVPTGD 104
                                    23        33        43        53        63        73        83        93       103 


Chain C from PDB  Type:PROTEIN  Length:86
 aligned with PRAX_HUMAN | Q9BXM0 from UniProtKB/Swiss-Prot  Length:1461

    Alignment length:86
                                    25        35        45        55        65        75        85        95      
           PRAX_HUMAN    16 LVEIIVETEAQTGVSGINVAGGGKEGIFVRELREDSPAARSLSLQEGDQLLSARVFFENFKYEDALRLLQCAEPYKVSFCLKRTVP 101
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeee.......eeeee...hhhhhhh..................hhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PDZ  PDB: C:16-85 UniProt: 16-85                                      ---------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4cmz C  16 LVEIIVETEAQTGVSGINVAGGGKEGIFVRELREDSPAARSLSLQEGDQLLSARVFFENFKYEDALRLLQCAEPYKVSFCLKRTVP 101
                                    25        35        45        55        65        75        85        95
   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 4CMZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CMZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CMZ)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (PRAX_HUMAN | Q9BXM0)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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).
biological process
    GO:0008366    axon ensheathment    Any process in which the axon of a neuron is insulated, and that insulation maintained, thereby preventing dispersion of the electrical signal.
    GO:0021675    nerve development    The process whose specific outcome is the progression of a nerve over time, from its formation to the mature structure.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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.

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