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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ACTIN-CROSSLINKING CORE OF SCHIZOSACCHAROMYCES POMBE FIMBRIN
 
Authors :  M. G. Klein, W. Shi, U. Ramagopal, Y. Tseng, D. Wirtz, D. R. Kovar, C. J. Staiger, S. C. Almo
Date :  10 Dec 03  (Deposition) - 22 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Filamentous Actin Binding Domain (Abd), Calponin Homology, Actin-Crosslinking, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. G. Klein, W. Shi, U. Ramagopal, Y. Tseng, D. Wirtz, D. R. Kovar, C. J. Staiger, S. C. Almo
Structure Of The Actin Crosslinking Core Of Fimbrin.
Structure V. 12 999 2004
PubMed-ID: 15274920  |  Reference-DOI: 10.1016/J.STR.2004.04.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIMBRIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-4T-1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentACTIN-CROSSLINKING CORE, AMINO ACIDS 108-614
    Organism CommonFISSION YEAST
    Organism ScientificSCHIZOSACCHAROMYCES POMBE
    Organism Taxid4896

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:217 , GLU A:218 , HIS A:219BINDING SITE FOR RESIDUE SO4 A 9001
2AC2SOFTWAREGLY A:202 , ARG A:230 , PRO A:262 , HIS A:405BINDING SITE FOR RESIDUE SO4 A 9002
3AC3SOFTWAREGLY A:211 , ASN A:454 , GLY A:472 , ALA A:473BINDING SITE FOR RESIDUE SO4 A 9003
4AC4SOFTWARETHR A:401 , TRP A:431BINDING SITE FOR RESIDUE SO4 A 9004
5AC5SOFTWARELYS A:432 , VAL A:434 , ASN A:435BINDING SITE FOR RESIDUE SO4 A 9005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RT8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RT8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RT8)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.FIMB_SCHPO112-233
261-364
385-495
508-614
  4A:112-233
A:261-364
A:385-495
A:508-614
2ACTININ_2PS00020 Actinin-type actin-binding domain signature 2.FIMB_SCHPO205-229  1A:205-229
3ACTININ_1PS00019 Actinin-type actin-binding domain signature 1.FIMB_SCHPO387-396  1A:387-396

(-) Exons   (0, 0)

(no "Exon" information available for 1RT8)

(-) 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:467
 aligned with FIMB_SCHPO | O59945 from UniProtKB/Swiss-Prot  Length:614

    Alignment length:505
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609     
           FIMB_SCHPO   110 INEEERREFIKHINSVLAGDPDVGSRVPINTETFEFFDQCKDGLILSKLINDSVPDTIDERVLNKQRNNKPLDNFKCIENNNVVINSAKAMGGISITNIGAGDILEGREHLILGLVWQIIRRGLLGKIDITLHPELYRLLEEDETLDQFLRLPPEKILLRWFNYHLKAANWPRTVSNFSKDVSDGENYTVLLNQLAPELCSRAPLQTTDVLQRAEQVLQNAEKLDCRKYLTPTAMVAGNPKLNLAFVAHLFNTHPGLEPLNEEEKPEIEPFDAEGEREARVFTLWLNSLDVTPSIHDFFNNLRDGLILLQAYDKITPNTVNWKKVNKAPASGDEMMRFKAVENCNYAVDLGKNQGFSLVGIQGADITDGSRTLTLALVWQMMRMNITKTLHSLSRGGKTLSDSDMVAWANSMAAKGGKGSQIRSFRDPSISTGVFVLDVLHGIKSEYVDYNLVTDGSTEELAIQNARLAISIARKLGAVIFILPEDIVAVRPRLVLHFIGSLMAV 614
               SCOP domains d1rt8a_ A: Fimbrin (Plastin), actin-crosslinking domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1rt8A01 A:110-237 Actin-binding Protein, T-fimbrin; domain 1                                                                                    1rt8A02 A:254-368 Actin-binding Protein, T-fimbrin; domain 1                                                                    1rt8A03 A:382-498 Actin-binding Protein, T-fimbrin; domain 1                                                         -1r      t8A04 A:500-614 Actin-binding Protein, T-fimbrin; domain 1                                                  CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CH-1rt8A01 A:511-614                                                                                     Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CH-1rt8A02 A:511-614                                                                                     Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CH-1rt8A03 A:511-614                                                                                     Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CH-1rt8A04 A:511-614                                                                                     Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhh......hhhhhhh..hhhhhhhhhhhh....hhhhh....---..hhhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhh....----------------hhhhhh..hhhhhhhhhhhhhhhhh.........hhhhh.hhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhh.....-------------hhhhhhhhhhhhhhhhh.......hhhhhh..hhhhhhhhhhhh....hhhhh..........hhhhhhhhhhhhhhhhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhhhhhh..------..hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --CH  PDB: A:112-233 UniProt: 112-233                                                                                       ---------------------------CH  PDB: A:261-364 UniProt: 261-364                                                                     --------------------CH  PDB: A:385-495 UniProt: 385-495                                                                            ------------CH  PDB: A:508-614 UniProt: 508-614                                                                         PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------ACTININ_2  PDB: A:205-229-------------------------------------------------------------------------------------------------------------------------------------------------------------ACTININ_1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rt8 A 110 INEEERREFIKHINSVLAGDPDVGSRVPINTETFEFFDQCKDGLILSKLINDSVPDTIDERVLNKQR---PLDNFKCIENNNVVINSAKAMGGISITNIGAGDILEGREHLILGLVWQIIRRGLLGKI----------------TLDQFLRLPPEKILLRWFNYHLKAANWPRTVSNFSKDVSDGENYTVLLNQLAPELCSRAPLQTTDVLQRAEQVLQNAEKLDCRKYLTPTAMVAGNPKLNLAFVAHLFNTHPGLEP-------------AEGEREARVFTLWLNSLDVTPSIHDFFNNLRDGLILLQAYDKITPNTVNWKKVNKAPASGDEMMRFKAVENCNYAVDLGKNQGFSLVGIQGADITDGSRTLTLALVWQMMRMNITKTLHS------TLSDSDMVAWANSMAAKGGKGSQIRSFRDPSISTGVFVLDVLHGIKSEYVDYNLVTDGSTEELAIQNARLAISIARKLGAVIFILPEDIVAVRPRLVLHFIGSLMAV 614
                                   119       129       139       149       159       169      |  -|      189       199       209       219       229       | -         -    |  259       269       279       289       299       309       319       329       339       349       359        |-         -  |    389       399       409       419       429       439       449       459       469       479       489       499 |     509       519       529       539       549       559       569       579       589       599       609     
                                                                                            176 180                                                      237              254                                                                                                               368           382                                                                                                                    501    508                                                                                                          

   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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: CH (43)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FIMB_SCHPO | O59945)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
biological process
    GO:0051666    actin cortical patch localization    Any process in which actin cortical patches are transported to, or maintained in, a specific location. An actin cortical patch is a discrete actin-containing structure found just beneath the plasma membrane in fungal cells.
    GO:0051764    actin crosslink formation    The process in which two or more actin filaments are connected together by proteins that act as crosslinks between the filaments. The crosslinked filaments may be on the same or differing axes.
    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: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:0030437    ascospore formation    The process in which cells that are products of meiosis acquire the specialized features of ascospores. Ascospores are generally found in clusters of four or eight spores within a single mother cell, the ascus, and are characteristic of the ascomycete fungi (phylum Ascomycota).
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0071963    establishment or maintenance of cell polarity regulating cell shape    Any cellular process that results in the specification, formation or maintenance of a polarized intracellular organization or cell growth patterns that regulate the shape of a cell.
    GO:1903475    mitotic actomyosin contractile ring assembly    Any actomyosin contractile ring assembly that is involved in mitotic cytokinesis.
    GO:0000281    mitotic cytokinesis    A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells.
    GO:0030835    negative regulation of actin filament depolymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of actin depolymerization.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0030479    actin cortical patch    An endocytic patch that consists of an actin-containing structure found at the plasma membrane in cells; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. An example of this is the actin cortical patch found in Saccharomyces cerevisiae.
    GO:0032432    actin filament bundle    An assembly of actin filaments that 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:0005826    actomyosin contractile ring    A cytoskeletal structure composed of actin filaments and myosin that forms beneath the plasma membrane of many cells, including animal cells and yeast cells, in a plane perpendicular to the axis of the spindle, i.e. the cell division plane. Ring contraction is associated with centripetal growth of the membrane that divides the cytoplasm of the two daughter cells. In animal cells, the contractile ring is located inside the plasma membrane at the location of the cleavage furrow. In budding fungal cells, e.g. mitotic S. cerevisiae cells, the contractile ring forms beneath the plasma membrane at the mother-bud neck before mitosis.
    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.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1aoa HOMO SAPIENS T-PLASTIN N-TERMINAL ACTIN BINDING DOMAIN
1pxy ARABIDOPSIS THALANIA FIMBRIN CROSSLINKING CORE