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(-) Description

Title :  STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN TUBBY-LIKE PROTEIN 1
 
Authors :  B. M. Hallberg, D. Ogg, C. Arrowsmith, H. Berglund, A. Edwards, M. Ehn, S S. Graslund, M. Hammarstrom, M. Hogbom, L. Holmberg-Schiavone, T. Ko P. Kursula, P. Nilsson-Ehle, P. Nordlund, T. Nyman, J. Sagemark, P. St M. Sundstrom, A. G. Thorsell, S. Van Den Berg, J. Weigelt, C. Persson
Date :  29 Dec 05  (Deposition) - 07 Feb 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tubby Filled-Barrel, Beta-Barrel, Filled-Beta-Roll, 12-Stranded-Beta- Barrel, Helix-Filled-Barrel, Retinitis Pigmentosa, Blindness, Structural Genomics, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Persson, D. Ogg, A. G. Thorsell, C. Arrowsmith, H. Berglund, A. Edwards, M. Ehn, S. Flodin, S. Graslund, M. Hammarstrom, M. Hogbom, L. Holmberg-Schiavone, T. Kotenyova, P. Kursula, P. Nilsson-Ehle, P. Nordlund, T. Nyman, J. Sagemark, P. Stenmark, M. Sundstrom, S. Van Den Berg, J. Weigelt, B. M. Hallberg
Structure Of The C-Terminal Domain Of Human Tubby-Like Protein 1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TUBBY RELATED PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPNIC-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTUBBY-LIKE PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
13DP1Ligand/Ion3-(N,N-DIMETHYLOCTYLAMMONIO)PROPANESULFONATE
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:249 , LEU A:408 , TYR A:448 , ARG A:466 , LEU B:321 , LEU B:322 , HOH B:1019BINDING SITE FOR RESIDUE 3DP A 1003
2AC2SOFTWAREARG A:250 , THR A:251 , ARG A:253BINDING SITE FOR RESIDUE SO4 A 1001
3AC3SOFTWAREARG B:258 , ARG B:455BINDING SITE FOR RESIDUE SO4 B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:467 -Pro A:468
2Tyr B:467 -Pro B:468

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 22)

Asymmetric/Biological Unit (11, 22)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_065500G368WTULP1_HUMANDisease (LCA15)387906837A/BG315W
02UniProtVAR_008278R378HTULP1_HUMANDisease (RP14)148749577A/BR325H
03UniProtVAR_037584F382STULP1_HUMANDisease (RP14)121909076A/BF329S
04UniProtVAR_065501R400WTULP1_HUMANDisease (LCA15)387906836A/BR347W
05UniProtVAR_007941R420PTULP1_HUMANDisease (RP14)121909073A/BR367P
06UniProtVAR_008279T454MTULP1_HUMANDisease (RP14)138200747A/BT401M
07UniProtVAR_007942I459KTULP1_HUMANDisease (RP14)121909075A/BI406K
08UniProtVAR_065502R482WTULP1_HUMANDisease (RP14)121909077A/BR429W
09UniProtVAR_008280K489RTULP1_HUMANDisease (RP14)62636511A/BK436R
10UniProtVAR_007943F491LTULP1_HUMANDisease (RP14)121909074A/BF438L
11UniProtVAR_008281A496TTULP1_HUMANUnclassified (RP14)141980901A/BA443T

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TUB_1PS01200 Tub family signature 1.TULP1_HUMAN479-492
 
  2A:426-439
B:426-439
2TUB_2PS01201 Tub family signature 2.TULP1_HUMAN527-542
 
  2A:474-483
B:474-483

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002297711aENSE00001785737chr6:35480715-35480589127TULP1_HUMAN1-16160--
1.2ENST000002297712ENSE00000849647chr6:35480467-3548041652TULP1_HUMAN16-33180--
1.3bENST000002297713bENSE00000747243chr6:35480047-3547995791TULP1_HUMAN34-64310--
1.4bENST000002297714bENSE00002193268chr6:35479583-35479425159TULP1_HUMAN64-117540--
1.5bENST000002297715bENSE00000747197chr6:35478787-35478638150TULP1_HUMAN117-167510--
1.6ENST000002297716ENSE00000747173chr6:35477705-35477604102TULP1_HUMAN167-201350--
1.7bENST000002297717bENSE00001885820chr6:35477527-35477411117TULP1_HUMAN201-240400--
1.8ENST000002297718ENSE00002201320chr6:35477089-35476986104TULP1_HUMAN240-274350--
1.9ENST000002297719ENSE00002178632chr6:35474056-354740516TULP1_HUMAN275-27620--
1.10aENST0000022977110aENSE00002159055chr6:35473950-35473780171TULP1_HUMAN277-333572A:238-280 (gaps)
B:238-280 (gaps)
43
43
1.11ENST0000022977111ENSE00002190679chr6:35473630-35473518113TULP1_HUMAN334-371382A:281-318 (gaps)
B:281-318 (gaps)
38
38
1.12cENST0000022977112cENSE00002194921chr6:35471625-35471514112TULP1_HUMAN371-408382A:318-355
B:318-355
38
38
1.13aENST0000022977113aENSE00002179188chr6:35471434-3547133699TULP1_HUMAN409-441332A:356-388 (gaps)
B:356-388
33
33
1.14bENST0000022977114bENSE00000747135chr6:35467929-35467758172TULP1_HUMAN442-499582A:389-446
B:389-446
58
58
1.15ENST0000022977115ENSE00000849646chr6:35466237-35465651587TULP1_HUMAN499-542442A:446-483
B:446-483
38
38

(-) 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:224
 aligned with TULP1_HUMAN | O00294 from UniProtKB/Swiss-Prot  Length:542

    Alignment length:246
                                   300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530      
          TULP1_HUMAN   291 PREFVLRPAPQGRTVRCRLTRDKKGMDRGMYPSYFLHLDTEKKVFLLAGRKRKRSKTANYLISIDPTNLSRGGENFIGKLRSNLLGNRFTVFDNGQNPQRGYSTNVASLRQELAAVIYETNVLGFRGPRRMTVIIPGMSAENERVPIRPRNASDGLLVRWQNKTLESLIELHNKPPVWNDDSGSYTLNFQGRVTQASVKNFQIVHADDPDYIVLQFGRVAEDAFTLDYRYPLCALQAFAIALSSFD 536
               SCOP domains d2fima_ A: automated ma       tches                                                                                                                                                                                                                    SCOP domains
               CATH domains 2fimA00 A:238-483 Tubby        Protein; Chain A                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.......eeeeeeee.-------..eeeeee.....eeeeeeee.......eeeee.....------.eeeeeee.....eeeee....hhhhh...hhhhh..eeeeeee.---------..eeeeee..................hhhhhhhhh....eeeeee...eee....eee..............eeee.........eeeeeee..eeeeee....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------W---------H---S-----------------W-------------------P---------------------------------M----K----------------------W------R-L----T---------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TUB_1         ----------------------------------TUB_2      PROSITE
           Transcript 1 (1) Exon 1.10a  PDB: A:238-280 (gaps)          Exon 1.11  PDB: A:281-318 (gaps)      -------------------------------------Exon 1.13a  PDB: A:356-388 (gaps)Exon 1.14b  PDB: A:389-446 UniProt: 442-499               ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------Exon 1.12c  PDB: A:318-355            ------------------------------------------------------------------------------------------Exon 1.15  PDB: A:446-483 [INCOMPLETE] Transcript 1 (2)
                 2fim A 238 PREFVLRPAPQGRTVRCRLTRDK-------YPSYFLHLDTEKKVFLLAGRKRKRSKTANYLISIDPTN------NFIGKLRSNLLGNRFTVFDNGQNPQRGYSTNVASLRQELAAVIYE---------RRMTVIIPGMSAENERVPIRPRNASDGLLVRWQNKTLESLIELHNKPPVWNDDSGSYTLNFQGRVTQASVKNFQIVHADDPDYIVLQFGRVAEDAFTLDYRYPLCALQAFAIALSSFD 483
                                   247       257  |      -|      277       287       297       | -    |  317       327       337       347        |-       367       377       387       397       407       417       427       437       447       457       467       477      
                                                260     268                                  305    312                                         356       366                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:232
 aligned with TULP1_HUMAN | O00294 from UniProtKB/Swiss-Prot  Length:542

    Alignment length:246
                                   300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530      
          TULP1_HUMAN   291 PREFVLRPAPQGRTVRCRLTRDKKGMDRGMYPSYFLHLDTEKKVFLLAGRKRKRSKTANYLISIDPTNLSRGGENFIGKLRSNLLGNRFTVFDNGQNPQRGYSTNVASLRQELAAVIYETNVLGFRGPRRMTVIIPGMSAENERVPIRPRNASDGLLVRWQNKTLESLIELHNKPPVWNDDSGSYTLNFQGRVTQASVKNFQIVHADDPDYIVLQFGRVAEDAFTLDYRYPLCALQAFAIALSSFD 536
               SCOP domains d2fimb_ B: automated matc     hes                                                                                                                                                                                                                      SCOP domains
               CATH domains 2fimB00 B:238-483 Tubby P     rotein; Chain A                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh.......eeeeeeee...-----..eeeeee......eeeeeee.......eeeee...---------..eeeee.....eeeeee...hhhhh...hhhhh..eeeeeeeee........eeeeeeee..................hhhhhhhh.....eeeeee...ee......ee..............eeee.........eeeeeee..eeeeee....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------W---------H---S-----------------W-------------------P---------------------------------M----K----------------------W------R-L----T---------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TUB_1         ----------------------------------TUB_2      PROSITE
           Transcript 1 (1) Exon 1.10a  PDB: B:238-280 (gaps)          Exon 1.11  PDB: B:281-318 (gaps)      -------------------------------------Exon 1.13a  PDB: B:356-388       Exon 1.14b  PDB: B:389-446 UniProt: 442-499               ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------Exon 1.12c  PDB: B:318-355            ------------------------------------------------------------------------------------------Exon 1.15  PDB: B:446-483 [INCOMPLETE] Transcript 1 (2)
                 2fim B 238 PREFVLRPAPQGRTVRCRLTRDKKG-----YPSYFLHLDTEKKVFLLAGRKRKRSKTANYLISIDP---------FIGKLRSNLLGNRFTVFDNGQNPQRGYSTNVASLRQELAAVIYETNVLGFRGPRRMTVIIPGMSAENERVPIRPRNASDGLLVRWQNKTLESLIELHNKPPVWNDDSGSYTLNFQGRVTQASVKNFQIVHADDPDYIVLQFGRVAEDAFTLDYRYPLCALQAFAIALSSFD 483
                                   247       257    |    -|      277       287       297     |   -     | 317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477      
                                                  262   268                                303       313                                                                                                                                                                          

   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  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TULP1_HUMAN | O00294)
molecular function
    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:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    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:0016358    dendrite development    The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0050908    detection of light stimulus involved in visual perception    The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal.
    GO:0042462    eye photoreceptor cell development    Development of a photoreceptor, a sensory cell in the eye that reacts to the presence of light. They usually contain a pigment that undergoes a chemical change when light is absorbed, thus stimulating a nerve.
    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:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    GO:0045494    photoreceptor cell maintenance    Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:1903546    protein localization to photoreceptor outer segment    A process in which a protein is transported to, or maintained in, a location within a photoreceptor outer segment.
    GO:0097500    receptor localization to non-motile cilium    A process in which a receptor is transported to, or maintained in, a location within a non-motile cilium.
    GO:0050896    response to stimulus    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 a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    GO:0060041    retina development in camera-type eye    The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
    GO:0001895    retina homeostasis    A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
    GO:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
    GO:0043679    axon terminus    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0001917    photoreceptor inner segment    The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs.
    GO:0001750    photoreceptor outer segment    The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes.
    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.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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

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        TULP1_HUMAN | O002943c5n

(-) Related Entries Specified in the PDB File

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