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(-) Description

Title :  CRYSTAL STRUCTURE OF HEDGEHOG-INTERACTING PROTEIN (HHIP)
 
Authors :  S. G. Hymowitz, I. Bosanac
Date :  01 Jun 09  (Deposition) - 23 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Receptor Ectodomain, Six-Bladed-Propeller Domain, Egf Domain, Disulfide Bond, Cell Membrane, Egf-Like Domain, Glycoprotein, Membrane, Secreted, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Bosanac, H. R. Maun, S. J. Scales, X. Wen, A. Lingel, J. F. Bazan, F. J. De Sauvage, S. G. Hymowitz, R. A. Lazarus
The Structure Of Shh In Complex With Hhip Reveals A Recognition Role For The Shh Pseudo Active Site In Signaling.
Nat. Struct. Mol. Biol. V. 16 691 2009
PubMed-ID: 19561609  |  Reference-DOI: 10.1038/NSMB.1632

(-) Compounds

Molecule 1 - HEDGEHOG-INTERACTING PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell LineINSECT CELLS
    Expression System PlasmidPENTR/D-TOPO WITH HONEYBEE MELITTIN SECRETION SIGNAL
    Expression System Taxid7111
    Expression System Vector TypeGATEWAY VECTOR PENTR/D-TOPO (INVITROGEN)
    FragmentUNP RESIDUES 193-667
    GeneHHIP, HHIP ORFNAMES: UNQ5825/PRO19644, HIP, UNQ5825/PRO19644
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHHIP, HIP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3HO4)

(-) SS Bonds  (22, 22)

Asymmetric Unit
No.Residues
1A:216 -A:536
2A:218 -A:543
3A:402 -A:624
4A:435 -A:452
5A:500 -A:594
6A:608 -A:617
7A:612 -A:623
8A:625 -A:634
9A:639 -A:649
10A:643 -A:655
11A:657 -A:666
12B:216 -B:536
13B:218 -B:543
14B:402 -B:624
15B:435 -B:452
16B:500 -B:594
17B:608 -B:617
18B:612 -B:623
19B:625 -B:634
20B:639 -B:649
21B:643 -B:655
22B:657 -B:666

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HO4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021518V341IHHIP_HUMANPolymorphism  ---A/BV341I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021518V341IHHIP_HUMANPolymorphism  ---AV341I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021518V341IHHIP_HUMANPolymorphism  ---BV341I

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

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_1PS00022 EGF-like domain signature 1.HHIP_HUMAN623-634
 
655-666
 
  4A:623-634
B:623-634
A:655-666
B:655-666
2EGF_2PS01186 EGF-like domain signature 2.HHIP_HUMAN623-634
 
655-666
 
  4A:623-634
B:623-634
A:655-666
B:655-666
3EGF_3PS50026 EGF-like domain profile.HHIP_HUMAN635-667
 
  2A:635-667
B:635-667
Biological Unit 1 (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_1PS00022 EGF-like domain signature 1.HHIP_HUMAN623-634
 
655-666
 
  2A:623-634
-
A:655-666
-
2EGF_2PS01186 EGF-like domain signature 2.HHIP_HUMAN623-634
 
655-666
 
  2A:623-634
-
A:655-666
-
3EGF_3PS50026 EGF-like domain profile.HHIP_HUMAN635-667
 
  1A:635-667
-
Biological Unit 2 (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_1PS00022 EGF-like domain signature 1.HHIP_HUMAN623-634
 
655-666
 
  2-
B:623-634
-
B:655-666
2EGF_2PS01186 EGF-like domain signature 2.HHIP_HUMAN623-634
 
655-666
 
  2-
B:623-634
-
B:655-666
3EGF_3PS50026 EGF-like domain profile.HHIP_HUMAN635-667
 
  1-
B:635-667

(-) Exons   (0, 0)

(no "Exon" information available for 3HO4)

(-) Sequences/Alignments

Asymmetric 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:437
 aligned with HHIP_HUMAN | Q96QV1 from UniProtKB/Swiss-Prot  Length:700

    Alignment length:456
                                   223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663      
           HHIP_HUMAN   214 HNCFCIQEVVSGLRQPVGALHSGDGSQRLFILEKEGYVKILTPEGEIFKEPYLDIHKLVQSGIKGGDERGLLSLAFHPNYKKNGKLYVSYTTNQERWAIGPHDHILRVVEYTVSRKNPHQVDLRTARVFLEVAELHRKHLGGQLLFGPDGFLYIILGDGMITLDDMEEMDGLSDFTGSVLRLDVDTDMCNVPYSIPRSNPHFNSTNQPPEVFAHGLHDPGRCAVDRHPTDININLTILCSDSNGKNRSSARILQIIKGKDYESEPSLLEFKPFSNGPLVGGFVYRGCQSERLYGSYVFGDRNGNFLTLQQSPVTKQWQEKPLCLGTSGSCRGYFSGHILGFGEDELGEVYILSSSKSMTQTHNGKLYKIVDPKRPLMPEECRATVQPAQTLTSECSRLCRNGYCTPTGKCCCSPGWEGDFCRTAKCEPACRHGGVCVRPNKCLCKKGYLGPQCEQV 669
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeee..eeeee........eeeee...eeeee...........ee................eeeeee..hhhhhheeeeeee.---------..eeeeeeeeee.......eeeeeeeeeeeeee......eeeeee.hhh.eeeee......hhhhhhh........eeeee............................eeee........eee..------.eeeeeee.......eeeeeee............eee.........eeee............eeee.....eeeeee......eeeeee..............eeeeeee.....eeeeee..----...eeeeeee.......hhhhh..........hhhhhhh..eee.....eee...ee.....ee..........eeee..eee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------I---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EGF_1       --------------------EGF_1       --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EGF_2       --------------------EGF_2       --- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EGF_3  PDB: A:635-667            -- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ho4 A 214 HNCFCIQEVVSGLRQPVGALHSGDGSQRLFILEKEGYVKILTPEGEIFKEPYLDIHKLVQSGIKGGDERGLLSLAFHPNYKKNGKLYVSYTT---------HDHILRVVEYTVSRKNPHQVDLRTARVFLEVAELHRKHLGGQLLFGPDGFLYIILGDGmITLDDmEEmDGLSDFTGSVLRLDVDTDmCNVPYSIPRSNPHFNSTNQPPEVFAHGLHDPGRCAVDRH------NLTILCSDSNGKNRSSARILQIIKGKDYESEPSLLEFKPFSNGPLVGGFVYRGCQSERLYGSYVFGDRNGNFLTLQQSPVTKQWQEKPLCLGTSGSCRGYFSGHILGFGEDELGEVYILSSSK----THNGKLYKIVDPKRPLmPEECRATVQPAQTLTSECSRLCRNGYCTPTGKCCCSPGWEGDFCRTAKCEPACRHGGVCVRPNKCLCKKGYLGPQCEHH 669
                                   223       233       243       253       263       273       283       293       303 |       - |     323       333       343       353       363       373     | 383       393       403       413       423       433      |  -   |   453       463       473       483       493       503       513       523       533       543       553       563     |   -|      583      |593       603       613       623       633       643       653       663      
                                                                                                                     305       315                                                       373-MSE |  |                401-MSE                                440    447                                                                                                                       569  574             590-MSE                                                                           
                                                                                                                                                                                               379-MSE                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                  382-MSE                                                                                                                                                                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:442
 aligned with HHIP_HUMAN | Q96QV1 from UniProtKB/Swiss-Prot  Length:700

    Alignment length:457
                                   223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       
           HHIP_HUMAN   214 HNCFCIQEVVSGLRQPVGALHSGDGSQRLFILEKEGYVKILTPEGEIFKEPYLDIHKLVQSGIKGGDERGLLSLAFHPNYKKNGKLYVSYTTNQERWAIGPHDHILRVVEYTVSRKNPHQVDLRTARVFLEVAELHRKHLGGQLLFGPDGFLYIILGDGMITLDDMEEMDGLSDFTGSVLRLDVDTDMCNVPYSIPRSNPHFNSTNQPPEVFAHGLHDPGRCAVDRHPTDININLTILCSDSNGKNRSSARILQIIKGKDYESEPSLLEFKPFSNGPLVGGFVYRGCQSERLYGSYVFGDRNGNFLTLQQSPVTKQWQEKPLCLGTSGSCRGYFSGHILGFGEDELGEVYILSSSKSMTQTHNGKLYKIVDPKRPLMPEECRATVQPAQTLTSECSRLCRNGYCTPTGKCCCSPGWEGDFCRTAKCEPACRHGGVCVRPNKCLCKKGYLGPQCEQVD 670
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..eeeee........eeeee...eeeee...........ee................eeeeee..hhhhhheeeeeee.---------..eeeeeeeeee.......eeeeeeeeeeeeee......eeeeee.hhh.eeeee......hhhhhhh........eeeee............................eeee........eee..------.eeeeeee.......eeeeeee.............ee.........eeee............eeee.....eeee..........eeee..............eeeeeee.....eeeeeehhhhhhh..eeeeeee.......hhhhh..........hhhhhhh................ee.....ee..........eeee..eee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EGF_1       --------------------EGF_1       ---- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EGF_2       --------------------EGF_2       ---- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EGF_3  PDB: B:635-667            --- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ho4 B 214 HNCFCIQEVVSGLRQPVGALHSGDGSQRLFILEKEGYVKILTPEGEIFKEPYLDIHKLVQSGIKGGDERGLLSLAFHPNYKKNGKLYVSYTT---------HDHILRVVEYTVSRKNPHQVDLRTARVFLEVAELHRKHLGGQLLFGPDGFLYIILGDGmITLDDmEEmDGLSDFTGSVLRLDVDTDmCNVPYSIPRSNPHFNSTNQPPEVFAHGLHDPGRCAVDRH------NLTILCSDSNGKNRSSARILQIIKGKDYESEPSLLEFKPFSNGPLVGGFVYRGCQSERLYGSYVFGDRNGNFLTLQQSPVTKQWQEKPLCLGTSGSCRGYFSGHILGFGEDELGEVYILSSSKSmTQTHNGKLYKIVDPKRPLmPEECRATVQPAQTLTSECSRLCRNGYCTPTGKCCCSPGWEGDFCRTAKCEPACRHGGVCVRPNKCLCKKGYLGPQCEHHH 670
                                   223       233       243       253       263       273       283       293       303 |       - |     323       333       343       353       363       373     | 383       393       403       413       423       433      |  -   |   453       463       473       483       493       503       513       523       533       543       553       563       573       583      |593       603       613       623       633       643       653       663       
                                                                                                                     305       315                                                       373-MSE |  |                401-MSE                                440    447                                                                                                                         571-MSE            590-MSE                                                                            
                                                                                                                                                                                               379-MSE                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                  382-MSE                                                                                                                                                                                                                                                                                            

   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  (0, 0)

(no "SCOP Domain" information available for 3HO4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HO4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HO4)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HHIP_HUMAN | Q96QV1)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0097108    hedgehog family protein binding    Interacting selectively and non-covalently with a member of the hedgehog protein family, signaling proteins involved in development.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016901    oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
    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:0048038    quinone binding    Interacting selectively and non-covalently with a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0009953    dorsal/ventral pattern formation    The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
    GO:0060441    epithelial tube branching involved in lung morphogenesis    The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.
    GO:0009968    negative regulation of signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
    GO:0045879    negative regulation of smoothened signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of smoothened signaling.
    GO:0007405    neuroblast proliferation    The expansion of a neuroblast population by cell division. A neuroblast is any cell that will divide and give rise to a neuron.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0040036    regulation of fibroblast growth factor receptor signaling pathway    Any process that modulates the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0048705    skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized.
    GO:0007224    smoothened signaling pathway    A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0060170    ciliary membrane    The portion of the plasma membrane surrounding a cilium.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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
        HHIP_HUMAN | Q96QV12wft 2wfx 2wg3 2wg4 3ho3 3ho5

(-) Related Entries Specified in the PDB File

3ho3 3ho5