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(-) Description

Title :  CRYSTAL STRUCTURE OF IHHN BOUND TO BOCFN3
 
Authors :  J. M. Kavran, D. J. Leahy
Date :  15 May 10  (Deposition) - 02 Jun 10  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym./Biol. Unit :  B,C
Keywords :  Binding Sites, Cell Adhesion Molecules, Cell Cycle Proteins, Cell Line, Conserved Sequence, Fibronectins, Hedgehog Proteins, Immunoglobulin G, Membrane Glycoproteins, Membrane Proteins, Protein Binding, Tertiary, Receptors, Cell Surface, Sequence Homology, Signal Transduction, Tumor Suppressor Proteins (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Kavran, M. D. Ward, O. O. Oladosu, S. Mulepati, D. J. Leahy
All Mammalian Hedgehog Proteins Interact With Cell Adhesion Molecule, Down-Regulated By Oncogenes (Cdo) And Brother Of Cdo (Boc) In A Conserved Manner.
J. Biol. Chem. V. 285 24584 2010
PubMed-ID: 20519495  |  Reference-DOI: 10.1074/JBC.M110.131680

(-) Compounds

Molecule 1 - INDIAN HEDGEHOG PROTEIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN-TERMINAL DOMAIN
    GeneIHH
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIHH, HHG-2, INDIAN HEDGEHOG PROTEIN N-PRODUCT, INDIAN HEDGEHOG PROTEIN C-PRODUCT
 
Molecule 2 - BROTHER OF CDO
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentTHIRD FN3 DOMAIN
    GeneBOC, UNQ604/PRO1190
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN BOC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit BC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:12 , HIS B:145 , ASP B:152 , GLU B:181 , HIS B:187BINDING SITE FOR RESIDUE ZN B 194
2AC2SOFTWAREGLU B:94 , GLU B:95 , ASP B:100 , THR B:130 , GLU B:131BINDING SITE FOR RESIDUE CA B 195
3AC3SOFTWAREHOH B:1 , HOH B:4 , HOH B:7 , GLU B:95 , GLU B:131 , ASP B:134 , ASP B:136BINDING SITE FOR RESIDUE CA B 196

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N1M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser B:53 -Pro B:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric/Biological Unit (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_015981P46LIHH_HUMANDisease (ACFD)121917856BP46L
2UniProtVAR_015982E95KIHH_HUMANDisease (BDA1)121917852BE95K
3UniProtVAR_015983D100EIHH_HUMANDisease (BDA1)121917854BD100E
4UniProtVAR_015984D100NIHH_HUMANDisease (BDA1)28936377BD100N
5UniProtVAR_015985E131KIHH_HUMANDisease (BDA1)121917853BE131K
6UniProtVAR_015986V190AIHH_HUMANDisease (ACFD)121917857BV190A
7UniProtVAR_035503V713MBOC_HUMANUnclassified367589886CV713M
8CancerSNPVAR_BOC_HUMAN_CCDS2971_1_01 *V713MBOC_HUMANDisease (Breast cancer)  ---CV713M
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.BOC_HUMAN474-571
608-703
712-812
  1-
-
C:712-812

(-) Exons   (0, 0)

(no "Exon" information available for 3N1M)

(-) 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 B from PDB  Type:PROTEIN  Length:155
 aligned with IHH_HUMAN | Q14623 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:155
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188     
            IHH_HUMAN    39 RPPRKLVPLAYKQFSPNVPEKTLGASGRYEGKIARSSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDRLNSLAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYGLLARLAVEAGFDWVYYESKAHVHCSVKSE 193
               SCOP domains d3n1mb_ B: automated matches                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains HH_signal-3n1mB01 B:39-189                                                                                                                             ---- Pfam domains
         Sec.struct. author .............ee......................hhhhhhee.....eee......hhh.eehhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhh.eeeeee...hhhhhhhhhhhhhhh...eeeeee..eeeee.... Sec.struct. author
             SAPs(SNPs) (1) -------L------------------------------------------------K----E------------------------------K----------------------------------------------------------A--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------N--------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n1m B  39 RPPRKLVPLAYKQFSPNVPEKTLGASGRYEGKIARSSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDRLNSLAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYGLLARLAVEAGFDWVYYESKAHVHCSVKSE 193
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188     

Chain C from PDB  Type:PROTEIN  Length:104
 aligned with BOC_HUMAN | Q9BWV1 from UniProtKB/Swiss-Prot  Length:1114

    Alignment length:104
                                   719       729       739       749       759       769       779       789       799       809    
            BOC_HUMAN   710 ERPVAGPYITFTDAVNETTIMLKWMYIPASNNNTPIHGFYIYYRPTDSDNDSDYKKDMVEGDKYWHSISHLQPETSYDIKMQCFNEGGESEFSNVMICETKARK 813
               SCOP domains d3n1mc_ C: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------fn3-3n1mC01 C:716-802                                                                  ----------- Pfam domains
         Sec.struct. author .......eeeeeeeee..eeeeeee.hhhhhh.....eeeeeeee....hhhhheeeeee....eeee.......eeeeeeeeee..ee......eeee..... Sec.struct. author
             SAPs(SNPs) (1) ---M---------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---M---------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --FN3  PDB: C:712-812 UniProt: 712-812                                                                 - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3n1m C 710 ERPVAGPYITFTDAVNETTIMLKWMYIPASNNNTPIHGFYIYYRPTDSDNDSDYKKDMVEGDKYWHSISHLQPETSYDIKMQCFNEGGESEFSNVMICETKARK 813
                                   719       729       739       749       759       769       779       789       799       809    

   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 3N1M)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: E-set (290)
(-)
Family: fn3 (66)

(-) Gene Ontology  (42, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (IHH_HUMAN | Q14623)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005113    patched binding    Interacting selectively and non-covalently with the patched (ptc) protein, a receptor for hedgehog proteins.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0042733    embryonic digit morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe.
    GO:0001947    heart looping    The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation.
    GO:0016539    intein-mediated protein splicing    The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues.
    GO:0060135    maternal process involved in female pregnancy    A reproductive process occurring in the mother that allows an embryo or fetus to develop within it.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0033085    negative regulation of T cell differentiation in thymus    Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation in the thymus.
    GO:0046639    negative regulation of alpha-beta T cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of alpha-beta T cell differentiation.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0033088    negative regulation of immature T cell proliferation in thymus    Any process that stops, prevents, or reduces the frequency, rate or extent of immature T cell proliferation in the thymus.
    GO:0009968    negative regulation of signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
    GO:0033089    positive regulation of T cell differentiation in thymus    Any process that activates or increases the frequency, rate or extent of T cell differentiation in the thymus.
    GO:0046638    positive regulation of alpha-beta T cell differentiation    Any process that activates or increases the frequency, rate or extent of alpha-beta T cell differentiation.
    GO:0032332    positive regulation of chondrocyte differentiation    Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation.
    GO:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:0045880    positive regulation of smoothened signaling pathway    Any process that activates or increases the frequency, rate or extent of smoothened signaling.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0045595    regulation of cell differentiation    Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
    GO:0032355    response to estradiol    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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0007224    smoothened signaling pathway    A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
    GO:0061053    somite development    The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
cellular component
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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.

Chain C   (BOC_HUMAN | Q9BWV1)
molecular function
    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:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0098779    positive regulation of macromitophagy in response to mitochondrial depolarization    The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
    GO:0051149    positive regulation of muscle cell differentiation    Any process that activates or increases the frequency, rate or extent of muscle cell differentiation.
    GO:0045663    positive regulation of myoblast differentiation    Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
    GO:0007224    smoothened signaling pathway    A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
cellular component
    GO:0044295    axonal growth cone    The migrating motile tip of a growing nerve cell axon.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BOC_HUMAN | Q9BWV13n1g 3n1p
        IHH_HUMAN | Q146233k7g 3k7h 3k7i 3k7j 3n1f 3n1o 3n1p

(-) Related Entries Specified in the PDB File

3d1m 3n1f 3n1g 3n1o 3n1p 3n1q 3n1r