Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF A EF-HAND DOMAIN FROM SEA URCHIN POLYCYSTIN-2
 
Authors :  I. Y. Kuo, C. Keeler, R. Corbin, A. Celic, E. T. Petri, M. E. Hodsdon, B. E.
Date :  22 Nov 13  (Deposition) - 08 Oct 14  (Release) - 05 Nov 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Ef-Hand, Channel, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Y. Kuo, C. Keeler, R. Corbin, A. Celic, E. T. Petri, M. E. Hodsdon, B. E. Ehrlich
The Number And Location Of Ef Hand Motifs Dictates The Calcium Dependence Of Polycystin-2 Function.
Faseb J. V. 28 2332 2014
PubMed-ID: 24558196  |  Reference-DOI: 10.1096/FJ.13-247106

(-) Compounds

Molecule 1 - POLYCYSTIC KIDNEY DISEASE PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Taxid: 562
    Gene: PKD2
    Organism Common: PURPLE URCHIN
    Organism Scientific: STRONGYLOCENTROTUS PURPURATUS
    Organism Taxid: 7668

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2MHH)

(-) Sites  (0, 0)

(no "Site" information available for 2MHH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2MHH)

(-) Exons   (0, 0)

(no "Exon" information available for 2MHH)

(-) Sequences/Alignments

NMR Structure
   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:96
 aligned with Q7Z2B5_STRPU | Q7Z2B5 from UniProtKB/TrEMBL  Length:907

    Alignment length:113
                                   635       645       655       665       675       685       695       705       715       725       735   
         Q7Z2B5_STRPU   626 SDIALQKSEFEITDYFKKGYEKMVGKINFKRDKIADIQEALAHADANADQHLDFDEWRQELKCRGHADADIEAVFAKYDVDGDRVLDAEEQMKMAHDLEGQKSDLNNQLAELE 738
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......h-------------hhhh----hhhhhhhhhhhhhh.........hhhhhhhhhhh.....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2mhh A  12 GGLVPRGS-------------HMAS----KRDKIADIQEALAHADANADQHLDFDEWRQELKCRGHADADIEAVFAKYDVDGDRVLDAEEQMKMAHDLEGQKSDLNNQLAELE 107
                                   | -         - |  |   24        34        44        54        64        74        84        94       104   
                                  19            20 23   24
   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 2MHH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (Q7Z2B5_STRPU | Q7Z2B5)
molecular function
    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+).
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:0050982    detection of mechanical stimulus    The series of events by which a mechanical stimulus is received and converted into a molecular signal.
cellular component
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2mhh)
 
  Sites
(no "Sites" information available for 2mhh)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2mhh)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2mhh
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q7Z2B5_STRPU | Q7Z2B5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q7Z2B5_STRPU | Q7Z2B5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 2MHH)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2MHH)