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 THE VILLIN HEADPIECE DOMAIN OF HUMAN ACTIN-BINDING LIM PROTEIN HOMOLOGUE (KIAA0843 PROTEIN)
 
Authors :  N. Tochio, S. Koshiba, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  11 Aug 03  (Deposition) - 11 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Vhp Domain, Actin Binding, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Tochio, S. Koshiba, T. Kigawa, S. Yokoyama
Solution Structure Of The Villin Headpiece Domain Of Human Actin-Binding Lim Protein Homologue (Kiaa0843 Protein)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACTIN-BINDING LIM PROTEIN HOMOLOGUE
    Chains: A
    Engineered: YES
    Expression System Plasmid: P020930-61
    Expression System Vector Type: PLASMID
    Fragment: VHP DOMAIN
    Gene: KAZUSA CDNA HK05155
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: KIAA0843 PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1UJS)

(-) Sites  (0, 0)

(no "Site" information available for 1UJS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UJS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UJS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UJS)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HPPS51089 Headpiece (HP) domain profile.ABLM3_HUMAN615-683  1A:14-82

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003098681cENSE00001878782chr5:148521066-148521217152ABLM3_HUMAN-00--
1.1gENST000003098681gENSE00001427228chr5:148521572-148521671100ABLM3_HUMAN1-550--
1.2aENST000003098682aENSE00001201072chr5:148563015-148563152138ABLM3_HUMAN5-51470--
1.3ENST000003098683ENSE00001201051chr5:148577782-148577965184ABLM3_HUMAN51-112620--
1.5aENST000003098685aENSE00001201047chr5:148579879-148579991113ABLM3_HUMAN112-150390--
1.6ENST000003098686ENSE00001201038chr5:148586571-148586697127ABLM3_HUMAN150-192430--
1.7ENST000003098687ENSE00001201031chr5:148590289-14859038294ABLM3_HUMAN192-223320--
1.8ENST000003098688ENSE00001201023chr5:148596522-14859660988ABLM3_HUMAN224-253300--
1.9ENST000003098689ENSE00001201016chr5:148610212-14861027059ABLM3_HUMAN253-272200--
1.10aENST0000030986810aENSE00001201012chr5:148612792-14861286372ABLM3_HUMAN273-296240--
1.11ENST0000030986811ENSE00001201007chr5:148617011-148617166156ABLM3_HUMAN297-348520--
1.12ENST0000030986812ENSE00001269114chr5:148618811-14861884030ABLM3_HUMAN349-358100--
1.13ENST0000030986813ENSE00001201000chr5:148619322-148619451130ABLM3_HUMAN359-402440--
1.15ENST0000030986815ENSE00001200997chr5:148620239-14862033799ABLM3_HUMAN402-435340--
1.16aENST0000030986816aENSE00001200993chr5:148622054-14862210148ABLM3_HUMAN435-451170--
1.17bENST0000030986817bENSE00001200990chr5:148624444-148624578135ABLM3_HUMAN451-496460--
1.18ENST0000030986818ENSE00001200988chr5:148626045-14862610965ABLM3_HUMAN496-517220--
1.19ENST0000030986819ENSE00001200983chr5:148627345-148627492148ABLM3_HUMAN518-567501A:1-77
1.20ENST0000030986820ENSE00001269072chr5:148629378-14862940730ABLM3_HUMAN567-577110--
1.21ENST0000030986821ENSE00001200975chr5:148630010-14863006859ABLM3_HUMAN577-596200--
1.22ENST0000030986822ENSE00001200967chr5:148630922-14863098261ABLM3_HUMAN597-617211A:8-169
1.23ENST0000030986823ENSE00001689480chr5:148631764-1486317718ABLM3_HUMAN617-61931A:16-183
1.24bENST0000030986824bENSE00001200957chr5:148632320-14863240081ABLM3_HUMAN620-646271A:19-4527
1.25dENST0000030986825dENSE00001890112chr5:148637854-1486400022149ABLM3_HUMAN647-683371A:46-8237

(-) 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:88
 aligned with ABLM3_HUMAN | O94929 from UniProtKB/Swiss-Prot  Length:683

    Alignment length:144
                                                                                                                                                                   683      
                                   555       565       575       585       595       605       615       625       635       645       655       665       675       | -    
          ABLM3_HUMAN   546 RSSTSSREALHTAGYEMSLNGSPRSHYLADSDPLISKSASLPAYRRNGLHRTPSADLFHYDSMNAVNWGMREYKIYPYELLLVTTRGRNRLPKDVDRTRLERHLSQEEFYQVFGMTISEFDRLALWKRNELKKQARLF------   -
               SCOP domains d1ujsa_                                                         A: Actin-binding LIM protein homologue KIAA0843                                  SCOP domains
               CATH domains 1ujsA00                                                         A:1-88 Villin Headpiece Domain; Chain A                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------VHP-1ujsA01 A:47-82                 ------ Pfam domains
         Sec.struct. author .......--------------------------------------------------------...................................hhhhhh..hhhhhhhh.hhhhhh..hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------HP  PDB: A:14-82 UniProt: 615-683                                    ------ PROSITE
           Transcript 1 (1) Exon 1.19  PDB: A:1-7 ---------Exon 1.21  PDB: -   Exon 1.22  PDB: A:8-1--Exon 1.24b  PDB: A:19-45   Exon 1.25d  PDB: A:46-82             ------ Transcript 1 (1)
           Transcript 1 (2) ---------------------Exon 1.20  ---------------------------------------1.2---------------------------------------------------------------------- Transcript 1 (2)
                 1ujs A   1 GSSGSSG--------------------------------------------------------NAVNWGMREYKIYPYELLLVTTRGRNRLPKDVDRTRLERHLSQEEFYQVFGMTISEFDRLALWKRNELKKQARLFSGPSSG  88
                                  |  -         -         -         -         -         -   |    14        24        34        44        54        64        74        84    
                                  7                                                        8
   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, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: VHP] (23)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (ABLM3_HUMAN | O94929)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0030032    lamellipodium assembly    Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0001725    stress fiber    A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.

 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 1ujs)
 
  Sites
(no "Sites" information available for 1ujs)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ujs)
 

(-) 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
  1ujs
    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
  ABLM3_HUMAN | O94929
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  ABLM3_HUMAN | O94929
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ABLM3_HUMAN | O94929: 2dj7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1UJS)