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

(-) Description

Title :  CRYSTAL STRUCTURE OF SPIRE KIND DOMAIN IN COMPLEX WITH THE TAIL OF FMN2
 
Authors :  B. Kreutz, C. L. Vizcarra, A. A. Rodal, A. V. Toms, J. Lu, M. E. Quinlan, M.
Date :  22 Mar 11  (Deposition) - 06 Jul 11  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  C-Lobe Of Protein Kinases, Actin Nucleator, Fmn-Family Formins, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Vizcarra, B. Kreutz, A. Rodal, A. Toms, J. Lu, W. Zheng, M. Quinlan, M. Eck
Structure Of The Spire Kind Domain And Insights Into Its Interaction With Fmn-Family Formins
Proc. Natl. Acad. Sci. Usa 2011
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN SPIRE HOMOLOG 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET HISTT
    Expression System StrainBL21DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentKIND DOMAIN (UNP RESIDUES 20-237)
    GeneSPIRE1, KIAA1135, SPIR1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSPIR-1
 
Molecule 2 - FORMIN-2
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET GST
    Expression System StrainBL21DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentFSI DOMAIN (UNP RESIDUES 1701-1722)
    GeneFMN2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3R7G)

(-) Sites  (0, 0)

(no "Site" information available for 3R7G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R7G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R7G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R7G)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINDPS51377 KIND domain profile.SPIR1_HUMAN40-231  1A:40-231

(-) Exons   (0, 0)

(no "Exon" information available for 3R7G)

(-) 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:154
 aligned with SPIR1_HUMAN | Q08AE8 from UniProtKB/Swiss-Prot  Length:756

    Alignment length:195
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226     
         SPIR1_HUMAN     37 RDALSLEEILRLYNQPINEEQAWAVCYQCCGSLRAAARRRQPRHRVRSAAQIRVWRDGAVTLAPAADDAGEPPPVAGKLGYSQCMETEVIESLGIIIYKALDYGLKENEERELSPPLEQLIDHMANTVEADGSNDEGYEAAEEGLGDEDEKRKISAIRSYRDVMKLCAAHLPTESDAPNHYQAVCRALFAETMEL  231
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........hhh.eeee....eee.....---------------..hhhhhhhhhhhhhhhhhh......eee..hhhhhhhhhhhh....--------------------------...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---KIND  PDB: A:40-231 UniProt: 40-231                                                                                                                                                              PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3r7g A   37 RDALSLEEILRLYNQPINEEQAWAVCYQCCGSLRAAARRRQPRHRVRSAAQIRVWRDGAVTLAPAAD---------------QCMETEVIESLGIIIYKALDYGLKENEERELSPPLEQLIDHMANTVE--------------------------AIRSYRDVMKLCAAHLPTESDAPNHYQAVCRALFAETMEL  231
                                    46        56        66        76        86        96      |  -         -  |    126       136       146       156        |-         -         -     | 196       206       216       226     
                                                                                            103             119                                           165                        192                                       

Chain B from PDB  Type:PROTEIN  Length:19
 aligned with FMN2_HUMAN | Q9NZ56 from UniProtKB/Swiss-Prot  Length:1722

    Alignment length:19
                                  1713         
          FMN2_HUMAN   1704 YKIKPRHDSGIKAKISMKT 1722
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                3r7g B 1704 YKIKPRHDSGIKAKISMKT 1722
                                  1713         

   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 3R7G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R7G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R7G)

(-) Gene Ontology  (39, 55)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SPIR1_HUMAN | Q08AE8)
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:0045010    actin nucleation    The initial step in the formation of an actin filament, in which actin monomers combine to form a new filament. Nucleation is slow relative to the subsequent addition of more monomers to extend the filament.
    GO:0036089    cleavage furrow formation    Generation of the cleavage furrow, a shallow groove in the cell surface near the old metaphase plate that marks the site of cytokinesis. This process includes the recruitment and localized activation of signals such as RhoA at the site of the future furrow to ensure that furrowing initiates at the correct site in the cell.
    GO:0051295    establishment of meiotic spindle localization    The cell cycle process in which the directed movement of the meiotic spindle to a specific location in the cell occurs.
    GO:0070649    formin-nucleated actin cable assembly    The aggregation, arrangement and bonding together of a set of components to form a formin-nucleated actin cable. A formin-nucleated actin cable is an actin filament bundle that consists of short filaments organized into bundles of uniform polarity, and is nucleated by formins.
    GO:0046907    intracellular transport    The directed movement of substances within a cell.
    GO:0040038    polar body extrusion after meiotic divisions    The cell cycle process in which two small cells are generated, as byproducts destined to degenerate, as a result of the first and second meiotic divisions of a primary oocyte during its development to a mature ovum. One polar body is formed in the first division of meiosis and the other in the second division; at each division, the cytoplasm divides unequally, so that the polar body is of much smaller size than the developing oocyte. At the second division in which a polar body is formed, the polar body and the developing oocyte each contain a haploid set of chromosomes.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, 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.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0032154    cleavage furrow    The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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.

Chain B   (FMN2_HUMAN | Q9NZ56)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    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.
biological process
    GO:0051017    actin filament bundle assembly    The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
    GO:0006974    cellular response to DNA damage stimulus    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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0071456    cellular response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0051295    establishment of meiotic spindle localization    The cell cycle process in which the directed movement of the meiotic spindle to a specific location in the cell occurs.
    GO:0070649    formin-nucleated actin cable assembly    The aggregation, arrangement and bonding together of a set of components to form a formin-nucleated actin cable. A formin-nucleated actin cable is an actin filament bundle that consists of short filaments organized into bundles of uniform polarity, and is nucleated by formins.
    GO:0051758    homologous chromosome movement towards spindle pole involved in homologous chromosome segregation    The directed movement of homologous chromosomes from the center of the spindle towards the spindle poles, mediated by the shortening of microtubules attached to the chromosomes, that contributes to meiosis I.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0046907    intracellular transport    The directed movement of substances within a cell.
    GO:0016344    meiotic chromosome movement towards spindle pole    The cell cycle process in which the directed movement of chromosomes from the center of the spindle towards the spindle poles takes place, mediated by the shortening of microtubules attached to the chromosomes. This occurs during meiosis.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0042177    negative regulation of protein catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0048477    oogenesis    The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
    GO:0040038    polar body extrusion after meiotic divisions    The cell cycle process in which two small cells are generated, as byproducts destined to degenerate, as a result of the first and second meiotic divisions of a primary oocyte during its development to a mature ovum. One polar body is formed in the first division of meiosis and the other in the second division; at each division, the cytoplasm divides unequally, so that the polar body is of much smaller size than the developing oocyte. At the second division in which a polar body is formed, the polar body and the developing oocyte each contain a haploid set of chromosomes.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, 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.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005902    microvillus    Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

 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
(no "Ligands, Modified Residues, Ions" information available for 3r7g)
 
  Sites
(no "Sites" information available for 3r7g)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3r7g)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3r7g
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  FMN2_HUMAN | Q9NZ56
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  SPIR1_HUMAN | Q08AE8
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  FMN2_HUMAN | Q9NZ56
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SPIR1_HUMAN | Q08AE8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FMN2_HUMAN | Q9NZ562yle
        SPIR1_HUMAN | Q08AE82yle 2ylf 3rbw

(-) Related Entries Specified in the PDB File

3rbw