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(-) Description

Title :  THE STRUCTURE OF A YEAST DYN2-NUP159 COMPLEX AND THE MOLECULAR BASIS FOR THE DYNEIN LIGHT CHAIN - NUCLEAR PORE INTERACTION
 
Authors :  K. C. Slep, E. M. Romes
Date :  17 Feb 12  (Deposition) - 21 Mar 12  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Nucleoporin, Dynein Light Chain Fold, Peptide Binding, Nuclear Pore, Structural Protein-Transport Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Romes, A. Tripathy, K. C. Slep
Structure Of A Yeast Dyn2-Nup159 Complex And Molecular Basi For Dynein Light Chain-Nuclear Pore Interaction.
J. Biol. Chem. V. 287 15862 2012
PubMed-ID: 22411995  |  Reference-DOI: 10.1074/JBC.M111.336172

(-) Compounds

Molecule 1 - DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P2
    Expression System Strain: BL21 DE3 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DYN2, SLC1, YDR424C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: S288C
 
Molecule 2 - NUCLEOPORIN NUP159
    Chains: B, D
    Engineered: YES
    Fragment: UNP RESIDUES 1116-1126
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Synonym: NUCLEAR PORE PROTEIN NUP159
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4DS1)

(-) Sites  (0, 0)

(no "Site" information available for 4DS1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DS1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:55 -Thr A:56
2Asn C:55 -Thr C:56

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DS1)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DYNEIN_LIGHT_1PS01239 Dynein light chain type 1 signature.DYL1_YEAST58-72
 		  2A:58-72
C:58-72

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIL115C1YIL115C.1IX:148706-1443244383NU159_YEAST1-146014602B:1117-1126
D:1116-1126		10
11

(-) 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:86
 aligned with DYL1_YEAST | Q02647 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:86
                                    16        26        36        46        56        66        76        86      
          DYL1_YEAST      7 STPIVKASDITDKLKEDILTISKDALDKYQLERDIAGTVKKQLDVKYGNTWHVIVGKNFGSYVTHEKGHFVYFYIGPLAFLVFKTA   92
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------DYNEIN_LIGHT_1 -------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                4ds1 A    7 STPIVKASDITDKLKEDILTISKDALDKYQLERDIAGTVKKQLDVKYGNTWHVIVGKNFGSYVTHEKGHFVYFYIGPLAFLVFKTA   92
                                    16        26        36        46        56        66        76        86      


Chain B from PDB  Type:PROTEIN  Length:10
 aligned with NU159_YEAST | P40477 from UniProtKB/Swiss-Prot  Length:1460

    Alignment length:10
                                  1126
         NU159_YEAST   1117 YAESGIQTDL 1126
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
               Transcript 1 Exon 1.1   Transcript 1
                4ds1 B 1117 YAESGIQTDL 1126
                                  1126


Chain C from PDB  Type:PROTEIN  Length:86
 aligned with DYL1_YEAST | Q02647 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:86
                                    16        26        36        46        56        66        76        86      
          DYL1_YEAST      7 STPIVKASDITDKLKEDILTISKDALDKYQLERDIAGTVKKQLDVKYGNTWHVIVGKNFGSYVTHEKGHFVYFYIGPLAFLVFKTA   92
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeee..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------DYNEIN_LIGHT_1 -------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                4ds1 C    7 STPIVKASDITDKLKEDILTISKDALDKYQLERDIAGTVKKQLDVKYGNTWHVIVGKNFGSYVTHEKGHFVYFYIGPLAFLVFKTA   92
                                    16        26        36        46        56        66        76        86      


Chain D from PDB  Type:PROTEIN  Length:11
 aligned with NU159_YEAST | P40477 from UniProtKB/Swiss-Prot  Length:1460

    Alignment length:11
                                  1125 
         NU159_YEAST   1116 NYAESGIQTDL 1126
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
               Transcript 1 Exon 1.1    Transcript 1
                4ds1 D 1116 NYAESGIQTDL 1126
                                  1125
   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 4DS1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DS1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DS1)

(-) Gene Ontology  (36, 38)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (DYL1_YEAST | Q02647)
molecular function
    GO:0008574    ATP-dependent microtubule motor activity, plus-end-directed    Catalysis of movement along a microtubule toward the plus end, coupled to the hydrolysis of ATP.
    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.
biological process
    GO:0040001    establishment of mitotic spindle localization    The cell cycle process in which the directed movement of the mitotic spindle to a specific location in the cell occurs.
    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:0030473    nuclear migration along microtubule    The directed movement of the nucleus along microtubules within the cell, mediated by motor proteins.
    GO:0051292    nuclear pore complex assembly    The aggregation, arrangement and bonding together of a set of components to form a nuclear pore complex.
    GO:2000582    positive regulation of ATP-dependent microtubule motor activity, plus-end-directed    Any process that activates or increases the frequency, rate or extent of ATP-dependent microtubule motor activity, plus-end-directed.
    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.
cellular component
    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:0005881    cytoplasmic microtubule    Any microtubule in the cytoplasm of a cell.
    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.
    GO:0005643    nuclear pore    Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
    GO:1990429    peroxisomal importomer complex    A protein complex responsible for transporting proteins into the peroxisomal matrix. An example of this complex is Pex14 found in S. cerevisae which has 9 core components and 12 transient interaction partners.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

Chain B,D   (NU159_YEAST | P40477)
molecular function
    GO:0000774    adenyl-nucleotide exchange factor activity    Stimulates the hydrolysis and exchange of adenyl nucleotides by other proteins.
    GO:0005487    nucleocytoplasmic transporter activity    Enables the directed movement of substances between the nucleus and the cytoplasm of a cell.
    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).
biological process
    GO:0006607    NLS-bearing protein import into nucleus    The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0097064    ncRNA export from nucleus    The directed movement of a non-coding RNA transcript (ncRNA) from the nucleus to the cytoplasm.
    GO:0031081    nuclear pore distribution    Any process that establishes the spatial arrangement of nuclear pores within the nuclear envelope.
    GO:0016973    poly(A)+ mRNA export from nucleus    The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
    GO:0006611    protein export from nucleus    The directed movement of a protein from the nucleus into the cytoplasm.
    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:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
    GO:0000055    ribosomal large subunit export from nucleus    The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm.
    GO:0000056    ribosomal small subunit export from nucleus    The directed movement of a ribosomal small subunit from the nucleus into the cytoplasm.
    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.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005643    nuclear pore    Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
    GO:0044613    nuclear pore central transport channel    The central substructure of the nuclear pore complex (NPC), through which nucleocytoplasmic transport of RNAs, proteins and small molecules occurs. The central transport channel is filled with FG-nucleoporins, which form a selective barrier and provide a series of binding sites for transporter proteins. Characterized S. cerevisiae FG-nucleoporins include Nup159p, Nup145Np, Nup116p, Nup100p, Nsp1p, Nup57p, Nup49p, Nup42p, Nup53p, Nup59p/Asm4p, Nup60p and Nup1. Characterized vertebrate FG-nucleoporins include Nup214, Nup98, Nup62, Nup54, Nup58/45, NLP1, and Nup153.
    GO:0044614    nuclear pore cytoplasmic filaments    Filamentous extensions on cytoplasmic face of the nuclear pore complex (NPC). In S. cerevisiae, Nup159p, Nup82p, and Nup42p contribute to the cytoplasmic filaments. In vertebrates, Nup358 is a major component.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DYL1_YEAST | Q02647: 4ht6
        NU159_YEAST | P40477: 1xip 3pbp 3rrm 3tkn

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