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(-) Description

Title :  CLATHRIN TERMINAL DOMAIN COMPLEXED WITH PITSTOP 1
 
Authors :  H. Bulut, L. Von Kleist, W. Saenger, V. Haucke
Date :  25 Nov 10  (Deposition) - 17 Aug 11  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Endocytosis, Endocytosis Inhibition (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Von Kleist, W. Stahlschmidt, H. Bulut, K. Gromova, D. Puchkov, M. J. Robertson, K. A. Macgregor, N. Tomlin, A. Pechstein, N. Chau, M. Chircop, J. Sakoff, J. P. Von Kries, W. Saenger, H. Krausslich, O. Shupliakov, P. J. Robinson, A. Mccluskey, V. Haucke
Role Of The Clathrin Terminal Domain In Regulating Coated Pit Dynamics Revealed By Small Molecule Inhibition.
Cell(Cambridge, Mass. ) V. 146 471 2011
PubMed-ID: 21816279  |  Reference-DOI: 10.1016/J.CELL.2011.06.025

(-) Compounds

Molecule 1 - CLATHRIN HEAVY CHAIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN-TERMINAL DOMAIN, RESIDUES 1-364
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCLATHRIN HEAVY CHAIN ON CHROMOSOME 17, CLH-17

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4VH11Ligand/Ion2-(4-AMINOBENZYL)-1,3-DIOXO-2,3-DIHYDRO-1H-BENZO[DE]ISOQUINOLINE-5-SULFONATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:0 , GLY A:150 , SER A:171 , ALA A:172 , HOH A:2454BINDING SITE FOR RESIDUE PEG A1358
2AC2SOFTWARETRP A:164 , LEU A:183 , SER A:185 , ARG A:188 , VAL A:190 , GLN A:192 , GLY A:234BINDING SITE FOR RESIDUE PEG A1359
3AC3SOFTWAREHIS A:129 , HOH A:2181 , HOH A:2203 , HOH A:2455 , HOH A:2456BINDING SITE FOR RESIDUE GOL A1360
4AC4SOFTWARELYS A:227 , VAL A:248 , ASP A:249BINDING SITE FOR RESIDUE ACT A1361
5AC5SOFTWAREILE A:62 , ARG A:64 , ILE A:66 , LEU A:82 , GLN A:89 , PHE A:91 , ILE A:93 , LYS A:96 , GLN A:174 , HOH A:2007 , HOH A:2097 , HOH A:2103BINDING SITE FOR RESIDUE VH1 A1362

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XZG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XZG)

(-) Exons   (0, 0)

(no "Exon" information available for 2XZG)

(-) 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:358
 aligned with CLH1_HUMAN | Q00610 from UniProtKB/Swiss-Prot  Length:1675

    Alignment length:358
                             1                                                                                                                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349        
           CLH1_HUMAN     - -MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNL 357
               SCOP domains d2xzga1 A:0-330 automated matches                                                                                                                                                                                                                                                                                                          d2xzga2 A:331-357           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee.hhhh.hhhhh....eeeee..eeeeeeee..eeeeeeee.......eeee....eeee.....eeeeee..eeeeee....eeeeeee....eeeeee....eeeeee..eeeeee.......eeeee.hhhhh..eeeeeee.....eeeeeeeeee..eeeeeeeeee....eeeee...eeeeeee........eeeeeeeeee..eeeeeeee.............eeeee..........eeeeeee....eeeeee...eeeeee.....eeeeee.....eeeeeee....eeeeee...eeeeeee...hhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xzg A   0 FMAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNL 357
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349        

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CLH1_HUMAN | Q00610)
molecular function
    GO:0032051    clathrin light chain binding    Interacting selectively and non-covalently with a clathrin light chain.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0060071    Wnt signaling pathway, planar cell polarity pathway    The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity.
    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:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:1900126    negative regulation of hyaluronan biosynthetic process    Any process that stops, prevents or reduces the frequency, rate or extent of hyaluronan biosynthetic process.
    GO:1903077    negative regulation of protein localization to plasma membrane    Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to plasma membrane.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:0031623    receptor internalization    A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    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:0033572    transferrin transport    The directed movement of transferrin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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.
cellular component
    GO:0030118    clathrin coat    A membrane coat found on coated pits and some coated vesicles; consists of polymerized clathrin triskelions, each comprising three clathrin heavy chains and three clathrin light chains, linked to the membrane via one of the AP adaptor complexes.
    GO:0030132    clathrin coat of coated pit    The coat found on coated pits and the coated vesicles derived from coated pits; comprises clathrin and the AP-2 adaptor complex.
    GO:0030130    clathrin coat of trans-Golgi network vesicle    A clathrin coat found on a vesicle of the trans-Golgi network.
    GO:0071439    clathrin complex    A protein complex that consists of three clathrin heavy chains and three clathrin light chains, organized into a symmetrical three-legged structure called a triskelion. In clathrin-coated vesicles clathrin is the main component of the coat and forms a polymeric mechanical scaffold on the vesicle surface.
    GO:0030669    clathrin-coated endocytic vesicle membrane    The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
    GO:0005905    clathrin-coated pit    A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
    GO:0030136    clathrin-coated vesicle    A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    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:0036020    endolysosome membrane    The lipid bilayer surrounding an endolysosome. An endolysosome is a transient hybrid organelle formed by fusion of a late endosome with a lysosome.
    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:1903561    extracellular vesicle    Any vesicle that is part of the extracellular region.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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: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:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
    GO:0032588    trans-Golgi network membrane    The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CLH1_HUMAN | Q006104g55

(-) Related Entries Specified in the PDB File

2xzh CLATHRIN TERMINAL DOMAIN COMPLEXED WITH PITSTOP 2