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(-) Description

Title :  STRUCTURE OF N-TERMINAL ACTIN DEPOLYMERIZING FACTOR HOMOLOGY (ADF-H) DOMAIN OF HUMAN TWINFILIN-2
 
Authors :  J. M. Elkins, A. C. W. Pike, O. King, E. Salah, P. Savitsky, F. Von Delft, J. Weigelt, A. Edwards, C. H. Arrowsmith, M. Sundstrom, S. Knapp
Date :  30 Aug 07  (Deposition) - 16 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Actin Binding, Phosphorylation, Cofilin-Like, Cytoskeleton, Actin-Binding, Protein Tyrosine Kinase-9, Actin Depolymerizing Factor Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Elkins, A. C. W. Pike, O. King, E. Salah, P. Savitsky, F. Von Delft J. Weigelt, A. Edwards, C. H. Arrowsmith, M. Sundstrom, S. Knapp
Crystal Structure Of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain Of Human Twinfilin-2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TWINFILIN-2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    FragmentACTIN DEPOLYMERIZING FACTOR HOMOLOGY (ADF-H) DOMAIN 1, RESIDUES 6-137
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTWINFILIN-1-LIKE PROTEIN, A6-RELATED PROTEIN, HA6RP, PROTEIN TYROSINE KINASE 9-LIKE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2ZN3Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:-1 , HIS A:8 , GLU A:44 , HOH A:2157BINDING SITE FOR RESIDUE ZN A1138
2AC2SOFTWAREHIS A:116 , ASP A:119 , HIS A:137 , HOH A:2158BINDING SITE FOR RESIDUE ZN A1139
3AC3SOFTWAREGLU A:15 , GLU A:82 , HOH A:2160 , HOH A:2161BINDING SITE FOR RESIDUE ZN A1140
4AC4SOFTWARELYS A:14 , PHE A:17 , ARG A:21 , GLU A:111 , PHE A:112 , HOH A:2132BINDING SITE FOR RESIDUE EDO A1141

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042407R72CTWF2_HUMANPolymorphism35114109AR72C
2UniProtVAR_042408Q76RTWF2_HUMANPolymorphism35711542AQ76R
3UniProtVAR_042409A103TTWF2_HUMANUnclassified867679383AA103T

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADF_HPS51263 ADF-H domain profile.TWF2_HUMAN4-139
177-313
  1A:6-137
-

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003055331aENSE00001931654chr3:52273177-52273008170TWF2_HUMAN1-991A:-1-96
1.2ENST000003055332ENSE00001719725chr3:52269122-5226904578TWF2_HUMAN9-35271A:9-3527
1.3bENST000003055333bENSE00001648090chr3:52266138-52265960179TWF2_HUMAN35-94601A:35-9460
1.4ENST000003055334ENSE00001702468chr3:52265555-5226546096TWF2_HUMAN95-126321A:95-12632
1.5ENST000003055335ENSE00001661253chr3:52265247-52265143105TWF2_HUMAN127-161351A:127-13711
1.6bENST000003055336bENSE00002169913chr3:52265011-52264886126TWF2_HUMAN162-203420--
1.7ENST000003055337ENSE00002193046chr3:52264086-52263936151TWF2_HUMAN204-254510--
1.8ENST000003055338ENSE00002200058chr3:52263798-52263677122TWF2_HUMAN254-294410--
1.9bENST000003055339bENSE00001125151chr3:52263217-52262626592TWF2_HUMAN295-349550--

(-) 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:134
 aligned with TWF2_HUMAN | Q6IBS0 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:134
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    
           TWF2_HUMAN     4 QTGIHATEELKEFFAKARAGSVRLIKVVIEDEQLVLGASQEPVGRWDQDYDRAVLPLLDAQQPCYLLYRLDSQNAQGFEWLFLAWSPDNSPVRLKMLYAATRATVKKEFGGGHIKDELFGTVKDDLSFAGYQKH 137
               SCOP domains d2vaca_ A: automated matches                                                                                                           SCOP domains
               CATH domains 2vacA00 A:-1-137 Severin                                                                                                               CATH domains
               Pfam domains -------Cofilin_ADF-2vacA01 A:11-137                                                                                                    Pfam domains
         Sec.struct. author ....eehhhhhhhhhhhhhh...eeeeeee..eeeeeeee....hhhhhhhhhhhhhh.....eeeeeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------C---R--------------------------T---------------------------------- SAPs(SNPs)
                    PROSITE ADF_H  PDB: A:6-137 UniProt: 4-139                                                                                                     PROSITE
           Transcript 1 (1) 1.1a  -------------------------Exon 1.3b  PDB: A:35-94 UniProt: 35-94                      Exon 1.4  PDB: A:95-126         Exon 1.5    Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.2  PDB: A:9-35      ------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2vac A  -1 SMGIHATEELKEFFAKARAGSVRLIKVVIEDEQLVLGASQEPVGRWDQDYDRAVLPLLDAQQPCYLLYRLDSQNAQGFEWLFLAWSPDNSPVRLKMLYAATRATVKKEFGGGHIKDELFGTVKDDLSFAGYQKH 137
                             ||     13        23        33        43        53        63        73        83        93       103       113       123       133    
                             0|                                                                                                                                   
                              6                                                                                                                                   

   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/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: ADF (44)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TWF2_HUMAN | Q6IBS0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0003785    actin monomer binding    Interacting selectively and non-covalently with monomeric actin, also known as G-actin.
    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).
    GO:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
biological process
    GO:0051016    barbed-end actin filament capping    The binding of a protein or protein complex to the barbed (or plus) end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
    GO:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0071363    cellular response to growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.
    GO:0071300    cellular response to retinoic acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0030837    negative regulation of actin filament polymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of actin polymerization.
    GO:0045773    positive regulation of axon extension    Any process that activates or increases the frequency, rate or extent of axon extension.
    GO:0010592    positive regulation of lamellipodium assembly    Any process that increases the rate, frequency or extent of the formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0032956    regulation of actin cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0032532    regulation of microvillus length    A process that modulates the length of a microvillus.
    GO:0042989    sequestering of actin monomers    The selective interaction of actin monomers with specific molecules that inhibit their polymerization by preventing their access to other monomers.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0030016    myofibril    The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0032420    stereocilium    An actin-based protrusion from the apical surface of auditory and vestibular hair cells and of neuromast cells. These protrusions are supported by a bundle of cross-linked actin filaments (an actin cable), oriented such that the plus (barbed) ends are at the tip of the protrusion, capped by a tip complex which bridges to the plasma. Bundles of stereocilia act as mechanosensory organelles.

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