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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CAP-GLY DOMAIN OF HUMAN DYNACTIN-1 (P150-GLUED)
 
Authors :  S. Honnappa, F. K. Winkler, M. O. Steinmetz
Date :  05 Jul 06  (Deposition) - 12 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Microtubule Binding, Cytoskeleton Associated Protein, P150-Glued, Strand Swap, Eb1 And Clip-170 Binding Protein, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Honnappa, O. Okhrimenko, R. Jaussi, H. Jawhari, I. Jelesarov, F. K. Winkler, M. O. Steinmetz
Key Interaction Modes Of Dynamic +Tip Networks.
Mol. Cell V. 23 663 2006
PubMed-ID: 16949363  |  Reference-DOI: 10.1016/J.MOLCEL.2006.07.013

(-) Compounds

Molecule 1 - DYNACTIN-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCAP-GLY DOMAIN
    GeneDCTN1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym150 KDA DYNEIN-ASSOCIATED POLYPEPTIDE, DP-150, DAP-150, P150-GLUED, P135

 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 2HKN)

(-) Sites  (0, 0)

(no "Site" information available for 2HKN)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HKN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HKN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 16)

Asymmetric/Biological Unit (8, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071452F52LDCTN1_HUMANDisease (PERRYS)  ---A/BF52L
2UniProtVAR_015850G59SDCTN1_HUMANDisease (HMN7B)121909342A/BG59S
3UniProtVAR_063867G71ADCTN1_HUMANDisease (PERRYS)67586389A/BG71A
4UniProtVAR_063868G71EDCTN1_HUMANDisease (PERRYS)67586389A/BG71E
5UniProtVAR_063869G71RDCTN1_HUMANDisease (PERRYS)72466485A/BG71R
6UniProtVAR_063870T72PDCTN1_HUMANDisease (PERRYS)72466486A/BT72P
7UniProtVAR_063871Q74PDCTN1_HUMANDisease (PERRYS)72466487A/BQ74P
8UniProtVAR_071453Y78CDCTN1_HUMANDisease (PERRYS)  ---A/BY78C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CAP_GLY_1PS00845 CAP-Gly domain signature.DCTN1_HUMAN48-79
 
  2A:48-79
B:48-79
2CAP_GLY_2PS50245 CAP-Gly domain profile.DCTN1_HUMAN48-90
 
  2A:48-90
B:48-90

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.7aENST000003618747aENSE00001940242chr2:74607482-74607132351DCTN1_HUMAN1-11110--
1.9dENST000003618749dENSE00001606774chr2:74605372-74605127246DCTN1_HUMAN12-93822A:16-93 (gaps)
B:26-93
78
68
1.10bENST0000036187410bENSE00000762538chr2:74604853-7460477579DCTN1_HUMAN94-120272A:94-97
B:94-97
4
4
1.11aENST0000036187411aENSE00002160083chr2:74604593-7460455935DCTN1_HUMAN120-131120--
1.13aENST0000036187413aENSE00001408363chr2:74603889-7460386921DCTN1_HUMAN132-13870--
1.14cENST0000036187414cENSE00001744349chr2:74601467-7460145018DCTN1_HUMAN139-14460--
1.16cENST0000036187416cENSE00001426050chr2:74600075-7460005521DCTN1_HUMAN145-15170--
1.17eENST0000036187417eENSE00001261719chr2:74598855-74598664192DCTN1_HUMAN152-215640--
1.17hENST0000036187417hENSE00001261373chr2:74598303-74598106198DCTN1_HUMAN216-281660--
1.18ENST0000036187418ENSE00000762534chr2:74597952-74597748205DCTN1_HUMAN282-350690--
1.19ENST0000036187419ENSE00001261359chr2:74597671-7459759379DCTN1_HUMAN350-376270--
1.20ENST0000036187420ENSE00001261354chr2:74597472-74597313160DCTN1_HUMAN376-429540--
1.21ENST0000036187421ENSE00000762531chr2:74597196-74597092105DCTN1_HUMAN430-464350--
1.22aENST0000036187422aENSE00001261342chr2:74596618-74596427192DCTN1_HUMAN465-528640--
1.23ENST0000036187423ENSE00001261333chr2:74596341-74596225117DCTN1_HUMAN529-567390--
1.24aENST0000036187424aENSE00000762527chr2:74596007-74595855153DCTN1_HUMAN568-618510--
1.24cENST0000036187424cENSE00001261323chr2:74595258-74595098161DCTN1_HUMAN619-672540--
1.25ENST0000036187425ENSE00001694213chr2:74594991-74594823169DCTN1_HUMAN672-728570--
1.26ENST0000036187426ENSE00001758208chr2:74594547-7459447969DCTN1_HUMAN729-751230--
1.27ENST0000036187427ENSE00001726995chr2:74594234-7459417263DCTN1_HUMAN752-772210--
1.28aENST0000036187428aENSE00001199793chr2:74594059-74593910150DCTN1_HUMAN773-822500--
1.28cENST0000036187428cENSE00001199788chr2:74593747-74593586162DCTN1_HUMAN823-876540--
1.28fENST0000036187428fENSE00001777917chr2:74593502-74593371132DCTN1_HUMAN877-920440--
1.29cENST0000036187429cENSE00001714582chr2:74593145-74593020126DCTN1_HUMAN921-962420--
1.30aENST0000036187430aENSE00001805744chr2:74592784-74592642143DCTN1_HUMAN963-1010480--
1.30eENST0000036187430eENSE00001635537chr2:74592368-74592202167DCTN1_HUMAN1010-1066570--
1.31bENST0000036187431bENSE00001749721chr2:74590755-7459074115DCTN1_HUMAN1066-107160--
1.31cENST0000036187431cENSE00001714864chr2:74590554-74590421134DCTN1_HUMAN1071-1115450--
1.32ENST0000036187432ENSE00001616375chr2:74590304-74590121184DCTN1_HUMAN1116-1177620--
1.33bENST0000036187433bENSE00001641035chr2:74589856-7458977780DCTN1_HUMAN1177-1203270--
1.34aENST0000036187434aENSE00001788775chr2:74589268-7458917990DCTN1_HUMAN1204-1233300--
1.35gENST0000036187435gENSE00001902273chr2:74588763-74588281483DCTN1_HUMAN1234-1278450--

(-) 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:76
 aligned with DCTN1_HUMAN | Q14203 from UniProtKB/Swiss-Prot  Length:1278

    Alignment length:82
                                    25        35        45        55        65        75        85        95  
           DCTN1_HUMAN   16 SRMSAEASARPLRVGSRVEVIGKGHRGTVAYVGATLFATGKWVGVILDEAKGKNDGTVQGRKYFTCDEGHGIFVRQSQIQVF 97
               SCOP domains d2hk      na_ A: Dynactin 1                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....------......eeeee...eeeeeeeee........eeeeee.........ee..ee........eeeehhh.eee. Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------L------S-----------AP-P---C------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------E-------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------------------------R-------------------------- SAPs(SNPs) (3)
                PROSITE (1) --------------------------------CAP_GLY_1  PDB: A:48-79         ------------------ PROSITE (1)
                PROSITE (2) --------------------------------CAP_GLY_2  PDB: A:48-90 UniProt: 48-90     ------- PROSITE (2)
               Transcript 1 Exon 1.9d  PDB: A:16-93 (gaps) UniProt: 12-93 [INCOMPLETE]                    1.10 Transcript 1
                  2hkn A 16 SHMS------PLRVGSRVEVIGKGHRGTVAYVGATLFATGKWVGVILDEAKGKNDGTVQGRKYFTCDEGHGIFVRQSQIQVF 97
                               |     -|       35        45        55        65        75        85        95  
                              19     26                                                                       

Chain B from PDB  Type:PROTEIN  Length:72
 aligned with DCTN1_HUMAN | Q14203 from UniProtKB/Swiss-Prot  Length:1278

    Alignment length:72
                                    35        45        55        65        75        85        95  
           DCTN1_HUMAN   26 PLRVGSRVEVIGKGHRGTVAYVGATLFATGKWVGVILDEAKGKNDGTVQGRKYFTCDEGHGIFVRQSQIQVF 97
               SCOP domains d2hknb_ B: Dynactin 1                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee...eeeeeeeeeee......eeeeeee.........ee..ee........eeeehhh.eee. Sec.struct. author
             SAPs(SNPs) (1) --------------------------L------S-----------AP-P---C------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------E-------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------R-------------------------- SAPs(SNPs) (3)
                PROSITE (1) ----------------------CAP_GLY_1  PDB: B:48-79         ------------------ PROSITE (1)
                PROSITE (2) ----------------------CAP_GLY_2  PDB: B:48-90 UniProt: 48-90     ------- PROSITE (2)
               Transcript 1 Exon 1.9d  PDB: B:26-93 UniProt: 12-93 [INCOMPLETE]                 1.10 Transcript 1
                  2hkn B 26 PLRVGSRVEVIGKGHRGTVAYVGATLFATGKWVGVILDEAKGKNDGTVQGRKYFTCDEGHGIFVRQSQIQVF 97
                                    35        45        55        65        75        85        95  

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HKN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HKN)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DCTN1_HUMAN | Q14203)
molecular function
    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).
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    GO:0036498    IRE1-mediated unfolded protein response    A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
    GO:0019886    antigen processing and presentation of exogenous peptide antigen via MHC class II    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    GO:0032402    melanosome transport    The directed movement of melanosomes into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0042147    retrograde transport, endosome to Golgi    The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport.
    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:0010970    transport along microtubule    The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity.
cellular component
    GO:0031252    cell leading edge    The area of a motile cell closest to the direction of movement.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    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.
    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:0005869    dynactin complex    A 20S multiprotein assembly of total mass about 1.2 MDa that activates dynein-based activity in vivo. A large structural component of the complex is an actin-like 40 nm filament composed of actin-related protein, to which other components attach.
    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:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0030904    retromer complex    A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35.
    GO:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DCTN1_HUMAN | Q142031txq 2coy 2hkq 2hl3 2hl5 2hqh 3e2u 3tq7

(-) Related Entries Specified in the PDB File

1txq 2coy 2hkq 2hl3 2hl5