Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF RAT PROFILIN 2A
 
Authors :  T. Haikarainen, P. Kursula
Date :  17 Dec 07  (Deposition) - 10 Feb 09  (Release) - 07 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Profilin, Cytoplasm, Acetylation, Cytoskeleton, Actin-Binding, Disulfide Bridge, Alternative Splicing, Protein-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Haikarainen, W. Q. Chen, G. Lubec, P. Kursula
Structure, Modifications And Ligand-Binding Properties Of Rat Profilin 2A.
Acta Crystallogr. , Sect. D V. 65 303 2009
PubMed-ID: 19307711  |  Reference-DOI: 10.1107/S0907444909000699

(-) Compounds

Molecule 1 - PROFILIN-2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T-2
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: DISULFIDE BRIDGE BETWEEN CYS15 AND CYS16
    Synonym: PROFILIN IIA, PROFILIN 2A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1DTU2Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
2GOL2Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:25 , GLY A:106 , HOH A:2217BINDING SITE FOR RESIDUE DTU A1140
2AC2SOFTWARECYS A:12 , PHE A:59 , THR A:60 , HOH A:2218BINDING SITE FOR RESIDUE DTU A1141
3AC3SOFTWAREGLY A:-2 , SER A:-1 , GLY A:2 , TRP A:3 , TYR A:6 , TYR A:133 , LEU A:134 , GOL A:1143 , HOH A:2050 , HOH A:2219 , HOH A:2220BINDING SITE FOR RESIDUE GOL A1142
4AC4SOFTWAREGLY A:-2 , GLN A:17 , GLU A:95 , TYR A:98 , MET A:113 , SER A:137 , GOL A:1142 , HOH A:2050BINDING SITE FOR RESIDUE GOL A1143
5AC5SOFTWAREARG A:104 , ARG A:135BINDING SITE FOR RESIDUE SO4 A1144

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:15 -A:16

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:91 -Gln A:92
2Gln A:92 -Gly A:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VK3)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROFILINPS00414 Profilin signature.PROF2_RAT1-9  1A:0-8

(-) Exons   (0, 0)

(no "Exon" information available for 2VK3)

(-) Sequences/Alignments

Asymmetric/Biological 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:142
 aligned with PROF2_RAT | Q9EPC6 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:142
                              1                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138  
            PROF2_RAT     - --MAGWQSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPAEIDVIIGKDREGFFTNGLTLGGKKCSVIRDSLYVDSDCTMDIRTKSQGGEPTYNVAVGRAGRVLVFVMGKEGVHGGGLNKKAYSMAKYLRDSGF 140
               SCOP domains d2vk3a_ A: automated matches                                                                                                                   SCOP domains
               CATH domains 2vk3A00 A:-2-139 Dynein light chain 2a, cytoplasmic                                                                                            CATH domains
               Pfam domains ----Profilin-2vk3A01 A:2-134                                                                                                             ----- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.eeeeeeee......eeee....hhhhhhhhhhhhhhh...hhhhhhheee..eeeeeeee........eeeeee.........eeeeee...eeeeeee....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --PROFILIN ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vk3 A  -2 GSMAGWQSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPAEIDVIIGKDREGFFTNGLTLGGKKCSVIRDSLYVDSDCTMDIRTKSQGGEPTYNVAVGRAGRVLVFVMGKEGVHGGGLNKKAYSMAKYLRDSGF 139
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137
   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)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PF (25)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PROF2_RAT | Q9EPC6)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
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:0032233    positive regulation of actin filament bundle assembly    Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles.
    GO:0030833    regulation of actin filament polymerization    Any process that modulates the frequency, rate or extent of the assembly of actin filaments by the addition of actin monomers to a filament.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  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
    DTU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:92 - Gly A:93   [ RasMol ]  
    Ser A:91 - Gln A:92   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  2vk3
    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
  PROF2_RAT | Q9EPC6
    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
  PROF2_RAT | Q9EPC6
    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 2VK3)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2VK3)