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(-) Description

Title :  CRYSTAL STRUCTURE OF APO-LC8
 
Authors :  G. Benison, P. A. Karplus, E. Barbar, M. Chiodo
Date :  21 Dec 07  (Deposition) - 02 Dec 08  (Release) - 02 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dimer, Cytoplasm, Dynein, Microtubule, Motor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Benison, P. A. Karplus, E. Barbar
The Interplay Of Ligand Binding And Quaternary Structure In The Diverse Interactions Of Dynein Light Chain Lc8.
J. Mol. Biol. V. 384 954 2008
PubMed-ID: 18948118  |  Reference-DOI: 10.1016/J.JMB.2008.09.083
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Vector TypePLASMID
    GeneCTP, CDLC1, DDLC1
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Synonym8 KDA DYNEIN LIGHT CHAIN, CUT UP PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:15 , ARG A:71 , HOH A:168 , HOH A:200BINDING SITE FOR RESIDUE ACT A 91
2AC2SOFTWAREGLY A:59 , ARG A:60 , ASN A:61 , PHE A:62 , HOH A:114BINDING SITE FOR RESIDUE SO4 A 92

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:52 -Thr A:53

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DYNEIN_LIGHT_1PS01239 Dynein light chain type 1 signature.DYL1_DROME55-69  1A:55-69
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DYNEIN_LIGHT_1PS01239 Dynein light chain type 1 signature.DYL1_DROME55-69  2A:55-69

(-) Exons   (0, 0)

(no "Exon" information available for 3BRI)

(-) Sequences/Alignments

Asymmetric 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:87
 aligned with DYL1_DROME | Q24117 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:87
                                    12        22        32        42        52        62        72        82       
            DYL1_DROME    3 DRKAVIKNADMSEEMQQDAVDCATQALEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETRHFIYFYLGQVAILLFKSG 89
               SCOP domains d3bria_ A: Dynein light chain 1 (DLC1)                                                  SCOP domains
               CATH domains 3briA00 A:3-89 Protein Inhibitor Of Neuronal Nitric Oxide Synthase;                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeee........eeeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------DYNEIN_LIGHT_1 -------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  3bri A  3 DRKAVIKNADMSEEMQQDAVDCATQALEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETRHFIYFYLGQVAILLFKSG 89
                                    12        22        32        42        52        62        72        82       

   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 Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A   (DYL1_DROME | Q24117)
molecular function
    GO:0042623    ATPase activity, coupled    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction directly drives some other reaction, for example ion transport across a membrane.
    GO:0045505    dynein intermediate chain binding    Interacting selectively and non-covalently with an intermediate chain of the dynein complex.
    GO:0051959    dynein light intermediate chain binding    Interacting selectively and non-covalently with a light intermediate chain of the dynein complex.
    GO:0003774    motor activity    Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
    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: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:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0022416    chaeta development    The process whose specific outcome is the progression of a chaeta over time, from its formation to the mature structure. A chaeta is a sensory multicellular cuticular outgrowth of a specifically differentiated cell.
    GO:0008407    chaeta morphogenesis    The process in which the anatomical structures of the chaeta are generated and organized. A chaeta is a sensory multicellular cuticular outgrowth of a specifically differentiated cell.
    GO:0000132    establishment of mitotic spindle orientation    A cell cycle process that sets the alignment of mitotic spindle relative to other cellular structures.
    GO:0007476    imaginal disc-derived wing morphogenesis    The process in which the anatomical structures of the imaginal disc-derived wing are generated and organized. The wing is an appendage modified for flying.
    GO:0034454    microtubule anchoring at centrosome    Any process in which a microtubule is maintained in a specific location in a cell by attachment to a centrosome.
    GO:0007018    microtubule-based movement    A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
    GO:0007017    microtubule-based process    Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
    GO:0022008    neurogenesis    Generation of cells within the nervous system.
    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:1904801    positive regulation of neuron remodeling    Any process that activates or increases the frequency, rate or extent of neuron remodeling.
    GO:0035071    salivary gland cell autophagic cell death    The stage-specific programmed cell death of salivary gland cells during salivary gland histolysis.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    GO:0007291    sperm individualization    The resolution of the male germline syncytium or cyst into individual gametes by packaging each spermatid into its own plasma membrane.
    GO:0007290    spermatid nucleus elongation    The change in shape of the spermatid nucleus from a spherical structure to an elongated organelle, during the latter part of spermatid differentiation.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0035220    wing disc development    Progression of the wing disc over time, from its initial formation through to its metamorphosis to form adult structures including the wing hinge, wing blade and pleura.
cellular component
    GO:0005814    centriole    A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005868    cytoplasmic dynein complex    Any dynein complex with a homodimeric dynein heavy chain core that catalyzes movement along a microtubule. Cytoplasmic dynein complexes participate in many cytoplasmic transport activities in eukaryotes, such as mRNA localization, intermediate filament transport, nuclear envelope breakdown, apoptosis, transport of centrosomal proteins, mitotic spindle assembly, virus transport, kinetochore functions, and movement of signaling and spindle checkpoint proteins. Some complexes participate in intraflagellar transport. Subunits associated with the dynein heavy chain mediate association between dynein heavy chain and cargoes, and may include light chains and light intermediate chains.
    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:0030286    dynein complex    Any of several large complexes that contain two or three dynein heavy chains and several light chains, and have microtubule motor activity.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DYL1_DROME | Q241171rhw 2p2t 2pg1 3brl 3dvh 3dvp 3dvt 3e2b 3fm7 3glw 4qh7 4qh8 5e0l 5e0m

(-) Related Entries Specified in the PDB File

3brl