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(-) Description

Title :  MECHANISM FOR THE SELECTIVE INTERACTION OF C-TERMINAL EH-DOMAIN PROTEINS WITH SPECIFIC NPF-CONTAINING PARTNERS
 
Authors :  F. Kieken, M. Sharma, M. Jovic, S. S. Giridharan, N. Naslavsky, S. Capla P. L. Sorgen
Date :  11 Jan 10  (Deposition) - 26 Jan 10  (Release) - 05 May 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
Keywords :  Ehd1, Endocytic Recycling, Protein-Protein Interactions, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Kieken, M. Sharma, M. Jovic, S. S. Giridharan, N. Naslavsky, S. Caplan, P. L. Sorgen
Mechanism For The Selective Interaction Of C-Terminal Eps15 Homology Domain Proteins With Specific Asn-Pro-Phe-Containing Partners.
J. Biol. Chem. V. 285 8687 2010
PubMed-ID: 20106972  |  Reference-DOI: 10.1074/JBC.M109.045666

(-) Compounds

Molecule 1 - EH DOMAIN-CONTAINING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPGEX6P-2
    FragmentC-TERMINAL DOMAIN (UNP RESIDUES 435-534)
    GeneEHD1, PAST, PAST1, CDABP0131
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTESTILIN, HPAST1
 
Molecule 2 - MICAL L1 LIKE PEPTIDE
    ChainsB
    EngineeredYES
    SynonymMOLECULE INTERACTING WITH RAB13, MIRAB13
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:94 , ASP A:96 , ASP A:98 , LEU A:100 , GLU A:105BINDING SITE FOR RESIDUE CA A 141

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EHPS50031 EH domain profile.EHD1_HUMAN444-532  1A:49-137
2EF_HAND_2PS50222 EF-hand calcium-binding domain profile.EHD1_HUMAN476-511  1A:81-116
3EF_HAND_1PS00018 EF-hand calcium-binding domain.EHD1_HUMAN489-501  1A:94-106

(-) Exons   (0, 0)

(no "Exon" information available for 2KSP)

(-) Sequences/Alignments

NMR Structure
   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:105
 aligned with EHD1_HUMAN | Q9H4M9 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:115
                                   429       439       449       459       469       479       489       499       509       519       529     
           EHD1_HUMAN   420 GPFGHGYGEGAGEGIDDVEWVVGKDKPTYDEIFYTLSPVNGKITGANAKKEMVKSKLPNTVLGKIWKLADVDKDGLLDDEEFALANHLIKVKLEGHELPADLPPHLVPPSKRRHE 534
               SCOP domains d2ksp          a_ A: automated matches                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------efhand_3-2kspA01 A:44-138                                                                      - Pfam domains
         Sec.struct. author .....----------.....hhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.............hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------EH  PDB: A:49-137 UniProt: 444-532                                                       -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------EF_HAND_2  PDB: A:81-116            ----------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------EF_HAND_1    --------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2ksp A  35 GPLGS----------DDVEWVVGKDKPTYDEIFYTLSPVNGKITGANAKKEMVKSKLPNTVLGKIWKLADVDKDGLLDDEEFALANHLIKVKLEGHELPADLPPHLVPPSKRRHE 139
                                |    -     |  44        54        64        74        84        94       104       114       124       134     
                               39         40                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:15
 aligned with MILK1_HUMAN | Q8N3F8 from UniProtKB/Swiss-Prot  Length:863

    Alignment length:15
                                   428     
          MILK1_HUMAN   419 LESKPYNPFEEEEED 433
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ............... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 2ksp B 143 LESKPYNPFEEEEED 157
                                   152     

   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)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (50, 61)

NMR Structure(hide GO term definitions)
Chain A   (EHD1_HUMAN | Q9H4M9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    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:1990090    cellular response to nerve growth factor stimulus    A 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 nerve growth factor stimulus.
    GO:0042632    cholesterol homeostasis    Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
    GO:0032456    endocytic recycling    The directed movement of membrane-bounded vesicles from recycling endosomes back to the plasma membrane where they are recycled for further rounds of transport.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    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:0034383    low-density lipoprotein particle clearance    The process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
    GO:0031175    neuron projection development    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:0010886    positive regulation of cholesterol storage    Any process that increases the rate or extent of cholesterol storage. Cholesterol storage is the accumulation and maintenance in cells or tissues of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:2001137    positive regulation of endocytic recycling    Any process that activates or increases the frequency, rate or extent of endocytic recycling.
    GO:1901741    positive regulation of myoblast fusion    Any process that activates or increases the frequency, rate or extent of myoblast fusion.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0061512    protein localization to cilium    A process in which a protein is transported to, or maintained in, a location within a cilium.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0060170    ciliary membrane    The portion of the plasma membrane surrounding a cilium.
    GO:0020018    ciliary pocket membrane    That part of the plasma membrane found in the ciliary pocket (also called flagellar pocket).
    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:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    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:0005811    lipid droplet    An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
    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:0031095    platelet dense tubular network membrane    The lipid bilayer surrounding the platelet dense tubular network.
    GO:0055038    recycling endosome membrane    The lipid bilayer surrounding a recycling endosome.

Chain B   (MILK1_HUMAN | Q8N3F8)
molecular function
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0070300    phosphatidic acid binding    Interacting selectively and non-covalently with phosphatidic acid, any of a class of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:1990090    cellular response to nerve growth factor stimulus    A 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 nerve growth factor stimulus.
    GO:0032456    endocytic recycling    The directed movement of membrane-bounded vesicles from recycling endosomes back to the plasma membrane where they are recycled for further rounds of transport.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0031175    neuron projection development    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:0097320    plasma membrane tubulation    A membrane tubulation process occurring in a plasma membrane.
    GO:0036010    protein localization to endosome    A process in which a protein is transported to, or maintained in, a location within an endosome.
    GO:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    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: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:1990126    retrograde transport, endosome to plasma membrane    The directed movement of membrane-bounded vesicles from endosomes back to the plasma membrane, a trafficking pathway that promotes the recycling of internalized transmembrane proteins.
    GO:0032458    slow endocytic recycling    The directed movement of membrane-bounded vesicles from deep (non-peripheral) compartments endocytic compartments back to the plasma membrane 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.
cellular component
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0031902    late endosome membrane    The lipid bilayer surrounding a late endosome.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0055038    recycling endosome membrane    The lipid bilayer surrounding a recycling endosome.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EHD1_HUMAN | Q9H4M92jq6 2kff 2kfg 2kfh

(-) Related Entries Specified in the PDB File

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