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(-) Description

Title :  COILED-COIL OLIGOMERIZATION DOMAIN OF THE POLYCYSTIN TRANSIENT RECEPTOR POTENTIAL CHANNEL PKD2L1
 
Authors :  D. A. Yernool, K. M Molland
Date :  11 Aug 11  (Deposition) - 18 Jan 12  (Release) - 08 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Trimeric Coiled-Coil, Oligomerization Domain, C-Terminal Cytoplasmic Regulatory Domain, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. L. Molland, L. N. Paul, D. A. Yernool
Crystal Structure And Characterization Of Coiled-Coil Domai Of The Transient Receptor Potential Channel Pkd2L1.
Biochim. Biophys. Acta V. 1824 413 2011
PubMed-ID: 22193359  |  Reference-DOI: 10.1016/J.BBAPAP.2011.12.002

(-) Compounds

Molecule 1 - POLYCYSTIC KIDNEY DISEASE 2-LIKE 1 PROTEIN
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPEV-L8
    Expression System StrainBL21PLYSS
    Expression System Taxid511693
    Expression System Vector TypePLASMIND
    FragmentUNP RESIDUES 699-737
    GenePKD2L1, PKD2L, PKDL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPOLYCYSTIN-2 HOMOLOG, POLYCYSTIN-2L1, POLYCYSTIN-L, POLYCYSTIN-L1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)ABC   
Biological Unit 2 (1x)   DEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3TE3)

(-) Sites  (0, 0)

(no "Site" information available for 3TE3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TE3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TE3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TE3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TE3)

(-) Exons   (0, 0)

(no "Exon" information available for 3TE3)

(-) 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:34
 aligned with PK2L1_HUMAN | Q9P0L9 from UniProtKB/Swiss-Prot  Length:805

    Alignment length:34
                                   709       719       729    
          PK2L1_HUMAN   700 GWVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGS 733
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                 3te3 A 700 GWVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGS 733
                                   709       719       729    

Chain B from PDB  Type:PROTEIN  Length:35
 aligned with PK2L1_HUMAN | Q9P0L9 from UniProtKB/Swiss-Prot  Length:805

    Alignment length:35
                                   710       720       730     
          PK2L1_HUMAN   701 WVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGSKL 735
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 3te3 B 701 WVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGSKL 735
                                   710       720       730     

Chain C from PDB  Type:PROTEIN  Length:37
 aligned with PK2L1_HUMAN | Q9P0L9 from UniProtKB/Swiss-Prot  Length:805

    Alignment length:37
                                   710       720       730       
          PK2L1_HUMAN   701 WVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGSKLKM 737
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 3te3 C 701 WVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGSKLKM 737
                                   710       720       730       

Chain D from PDB  Type:PROTEIN  Length:34
 aligned with PK2L1_HUMAN | Q9P0L9 from UniProtKB/Swiss-Prot  Length:805

    Alignment length:34
                                   709       719       729    
          PK2L1_HUMAN   700 GWVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGS 733
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                 3te3 D 700 GWVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGS 733
                                   709       719       729    

Chain E from PDB  Type:PROTEIN  Length:33
 aligned with PK2L1_HUMAN | Q9P0L9 from UniProtKB/Swiss-Prot  Length:805

    Alignment length:33
                                   708       718       728   
          PK2L1_HUMAN   699 GGWVSGEEFYMLTRRVLQLETVLEGVVSQIDAV 731
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 3te3 E 699 GGWVSGEEFYMLTRRVLQLETVLEGVVSQIDAV 731
                                   708       718       728   

Chain F from PDB  Type:PROTEIN  Length:38
 aligned with PK2L1_HUMAN | Q9P0L9 from UniProtKB/Swiss-Prot  Length:805

    Alignment length:38
                                   708       718       728        
          PK2L1_HUMAN   699 GGWVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGSKLK 736
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 3te3 F 699 GGWVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGSKLK 736
                                   708       718       728        

   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 3TE3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TE3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TE3)

(-) Gene Ontology  (38, 38)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (PK2L1_HUMAN | Q9P0L9)
molecular function
    GO:0051393    alpha-actinin binding    Interacting selectively and non-covalently with alpha-actinin, one of a family of proteins that cross-link F-actin as antiparallel homodimers. Alpha-actinin has a molecular mass of 93-103 KDa; at the N-terminus there are two calponin homology domains, at the C-terminus there are two EF-hands. These two domains are connected by the rod domain. This domain is formed by triple-helical spectrin repeats.
    GO:0005227    calcium activated cation channel activity    Enables the calcium concentration-regulatable energy-independent passage of cations across a lipid bilayer down a concentration gradient.
    GO:0005262    calcium channel activity    Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0015269    calcium-activated potassium channel activity    Enables the calcium concentration-regulatable energy-independent passage of potassium ions across a lipid bilayer down a concentration gradient.
    GO:0005261    cation channel activity    Enables the energy-independent passage of cations across a lipid bilayer down a concentration gradient.
    GO:0008324    cation transmembrane transporter activity    Enables the transfer of cation from one side of the membrane to the other.
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0051371    muscle alpha-actinin binding    Interacting selectively and non-covalently with muscle isoforms of actinin. Muscle alpha-actinin isoforms are found in skeletal and cardiac muscle and are localized to the Z-disc.
    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:0005272    sodium channel activity    Enables the facilitated diffusion of a sodium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0033040    sour taste receptor activity    Combining with soluble sour compounds to initiate a change in cell activity. These receptors are responsible for the sense of sour taste.
biological process
    GO:0070588    calcium ion transmembrane transport    A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006816    calcium ion transport    The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006812    cation transport    The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0071468    cellular response to acidic pH    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution.
    GO:0001581    detection of chemical stimulus involved in sensory perception of sour taste    The series of events required for a sour taste stimulus to be received and converted to a molecular signal.
    GO:0050982    detection of mechanical stimulus    The series of events by which a mechanical stimulus is received and converted into a molecular signal.
    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:0071805    potassium ion transmembrane transport    A process in which a potassium ion is transported from one side of a membrane to the other.
    GO:0070207    protein homotrimerization    The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.
    GO:0050915    sensory perception of sour taste    The series of events required to receive a sour taste stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
    GO:0007224    smoothened signaling pathway    A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
    GO:0035725    sodium ion transmembrane transport    A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    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:0034704    calcium channel complex    An ion channel complex through which calcium ions pass.
    GO:0034703    cation channel complex    An ion channel complex through which cations pass.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0060170    ciliary membrane    The portion of the plasma membrane surrounding a cilium.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal 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: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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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