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(-) Description

Title :  MOLECULAR STRUCTURE OF THE ROD DOMAIN OF DICTYOSTELIUM FILAMIN
 
Authors :  G. M. Popowicz, R. Mueller, A. A. Noegel, M. Schleicher, R. Huber, T. A. Holak
Date :  27 Jun 04  (Deposition) - 05 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Abp-120, Filamin, Immunoglobulin Fold, Rod Domain, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. M. Popowicz, R. Mueller, A. A. Noegel, M. Schleicher, R. Huber, T. A. Holak
Molecular Structure Of The Rod Domain Of Dictyostelium Filamin
J. Mol. Biol. V. 342 1637 2004
PubMed-ID: 15364587  |  Reference-DOI: 10.1016/J.JMB.2004.08.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GELATION FACTOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPT7-7 , ECORI-SALI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentREPEAT 4,5,6 ROD DOMAIN
    GeneABPC
    Organism ScientificDICTYOSTELIUM DISCOIDEUM
    Organism Taxid44689
    SynonymACTIN BINDING PROTEIN 120, ABP-120, DDFILAMIN

 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 1WLH)

(-) Sites  (0, 0)

(no "Site" information available for 1WLH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe A:639 -Pro A:640
2Met A:741 -Pro A:742
3Ser A:831 -Pro A:832
4Phe B:639 -Pro B:640
5Met B:741 -Pro B:742
6Ser B:831 -Pro B:832

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FILAMIN_REPEATPS50194 Filamin/ABP280 repeat profile.GELA_DICDI245-346
346-446
446-545
546-645
646-747
 
763-837
 
  4-
-
-
-
A:646-747
B:646-747
A:763-837
B:763-837

(-) Exons   (0, 0)

(no "Exon" information available for 1WLH)

(-) 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:308
 aligned with GELA_DICDI | P13466 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:311
                                   556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856 
           GELA_DICDI   547 PAADPEKSYAEGPGLDGGECFQPSKFKIHAVDPDGVHRTDGGDGFVVTIEGPAPVDPVMVDNGDGTYDVEFEPKEAGDYVINLTLDGDNVNGFPKTVTVKPAPSAEHSYAEGEGLVKVFDNAPAEFTIFAVDTKGVARTDGGDPFEVAINGPDGLVVDAKVTDNNDGTYGVVYDAPVEGNYNVNVTLRGNPIKNMPIDVKCIEGANGEDSSFGSFTFTVAAKNKKGEVKTYGGDKFEVSITGPAEEITLDAIDNQDGTYTAAYSLVGNGRFSTGVKLNGKHIEGSPFKQVLGNPGKKNPEVKSFTTTRTAN 857
               SCOP domains d1wlha1 A:547-647 F-actin cross-link   ing gelation factor (ABP-120) repeats                         d1wlha2 A:648-749 F-actin cross-linking gelation factor (ABP-120) repeats                             d1wlha3 A:750-857 F-actin cross-linking gelation factor (ABP-120) repeats                                    SCOP domains
               CATH domains 1wlhA01 A:547-654 Immunoglobulins                                                                           1wlhA02 A:655-756 Immunoglobulins                                                                     1wlhA03 A:757-857 Immunoglobulins                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee......ee....eeeeee.......---.....eeeeee...............eeeeee......eeeeeeee.........eeeeee.........eehhhhh.ee....eeeeee...............eeeeee.........eeee....eeeeee.....eeeeeeeee..ee......eeeee...hhhhheeeeeeeeee...............eeeeee....eeeeeeee....eeeeeeeee..eeeeeeeee..ee.....eeeee.............eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FILAMIN_REPEAT  PDB: - UniProt: 546-645                                                            FILAMIN_REPEAT  PDB: A:646-747 UniProt: 646-747                                                       ---------------FILAMIN_REPEAT  PDB: A:763-837 UniProt: 763-837                            -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wlh A 547 PAADPEKSYAEGPGLDGGECFQPSKFKIHAVDPDGV---DGGDGFVVTIEGPAPVDPVMVDNGDGTYDVEFEPKEAGDYVINLTLDGDNVNGFPKTVTVKPAPSAEHSYAEGEGLVKVFDNAPAEFTIFAVDTKGVARTDGGDPFEVAINGPDGLVVDAKVTDNNDGTYGVVYDAPVEGNYNVNVTLRGNPIKNMPIDVKCIEGANGEDSSFGSFTFTVAAKNKKGEVKTYGGDKFEVSITGPAEEITLDAIDNQDGTYTAAYSLVGNGRFSTGVKLNGKHIEGSPFKQVLGNPGKKNPEVKSFTTTRTAN 857
                                   556       566       576     | 586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856 
                                                             582 586                                                                                                                                                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:306
 aligned with GELA_DICDI | P13466 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:309
                                   558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848         
           GELA_DICDI   549 ADPEKSYAEGPGLDGGECFQPSKFKIHAVDPDGVHRTDGGDGFVVTIEGPAPVDPVMVDNGDGTYDVEFEPKEAGDYVINLTLDGDNVNGFPKTVTVKPAPSAEHSYAEGEGLVKVFDNAPAEFTIFAVDTKGVARTDGGDPFEVAINGPDGLVVDAKVTDNNDGTYGVVYDAPVEGNYNVNVTLRGNPIKNMPIDVKCIEGANGEDSSFGSFTFTVAAKNKKGEVKTYGGDKFEVSITGPAEEITLDAIDNQDGTYTAAYSLVGNGRFSTGVKLNGKHIEGSPFKQVLGNPGKKNPEVKSFTTTRTAN 857
               SCOP domains d1wlhb1 B:549-647 F-actin cross-li   nking gelation factor (ABP-120) repeats                       d1wlhb2 B:648-749 F-actin cross-linking gelation factor (ABP-120) repeats                             d1wlhb3 B:750-857 F-actin cross-linking gelation factor (ABP-120) repeats                                    SCOP domains
               CATH domains 1wlhB01 B:549-654 Immunoglobulins                                                                         1wlhB02 B:655-756 Immunoglobulins                                                                     1wlhB03 B:757-857 Immunoglobulins                                                                     CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Filamin-1wlhB01 B:747-834                                                               ----------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Filamin-1wlhB02 B:747-834                                                               ----------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Filamin-1wlhB03 B:747-834                                                               ----------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Filamin-1wlhB04 B:747-834                                                               ----------------------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Filamin-1wlhB05 B:747-834                                                               ----------------------- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Filamin-1wlhB06 B:747-834                                                               ----------------------- Pfam domains (6)
         Sec.struct. author ......eee............eeeeee.......---.....ee..ee.......eee.....eeeeee......eeee..ee.........eeee..........eeehhhh.eee....eeeeee...............eeeeee.....ee..ee......eeeeee.....eeeeeeeee..ee.....eeeeee...hhhhheeeeeeeeee...............eeeeeee.eeeee..eee....eeeeeeeeee.eeeeeeeee.........eeeee............eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FILAMIN_REPEAT  PDB: - UniProt: 546-645                                                          FILAMIN_REPEAT  PDB: B:646-747 UniProt: 646-747                                                       ---------------FILAMIN_REPEAT  PDB: B:763-837 UniProt: 763-837                            -------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wlh B 549 ADPEKSYAEGPGLDGGECFQPSKFKIHAVDPDGV---DGGDGFVVTIEGPAPVDPVMVDNGDGTYDVEFEPKEAGDYVINLTLDGDNVNGFPKTVTVKPAPSAEHSYAEGEGLVKVFDNAPAEFTIFAVDTKGVARTDGGDPFEVAINGPDGLVVDAKVTDNNDGTYGVVYDAPVEGNYNVNVTLRGNPIKNMPIDVKCIEGANGEDSSFGSFTFTVAAKNKKGEVKTYGGDKFEVSITGPAEEITLDAIDNQDGTYTAAYSLVGNGRFSTGVKLNGKHIEGSPFKQVLGNPGKKNPEVKSFTTTRTAN 857
                                   558       568       578   |   588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848         
                                                           582 586                                                                                                                                                                                                                                                                               

   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, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: E-set (290)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GELA_DICDI | P13466)
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: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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
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:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0048870    cell motility    Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
    GO:0006972    hyperosmotic response    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or cell.
    GO:0044351    macropinocytosis    An endocytosis process that results in the uptake of liquid material by cells from their external environment by the 'ruffling' of the cell membrane to form heterogeneously sized intracellular vesicles called macropinosomes, which can be up to 5 micrometers in size.
    GO:0006909    phagocytosis    An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
    GO:0042331    phototaxis    The directed movement of a motile cell or organism in response to light.
    GO:0030587    sorocarp development    The process whose specific outcome is the progression of the sorocarp over time, from its formation to the mature structure. The process begins with the aggregation of individual cells and ends with the mature sorocarp. The sorocarp is a structure containing a spore-bearing sorus that sits on top of a stalk. An example of this process is found in Dictyostelium discoideum.
    GO:0043052    thermotaxis    The directed movement of a motile cell or organism in response to a temperature gradient. Movement may be towards either a higher or lower temperature.
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:0031252    cell leading edge    The area of a motile cell closest to the direction of movement.
    GO:0030864    cortical actin cytoskeleton    The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0001891    phagocytic cup    An invagination of the cell membrane formed by an actin dependent process during phagocytosis. Following internalization it is converted into a phagosome.
    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.

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  Cis Peptide Bonds
    Met A:741 - Pro A:742   [ RasMol ]  
    Met B:741 - Pro B:742   [ RasMol ]  
    Phe A:639 - Pro A:640   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        GELA_DICDI | P134661ksr 1qfh 2n62

(-) Related Entries Specified in the PDB File

1ksr REPEAT 4 NMR
1qfh REPEATS 5-6