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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF SECRETED FRIZZLED-RELATED PROTEIN 3 (SFRP-3;FZB)
 
Authors :  C. E. Dann Iii, J. C. Hsieh, A. Rattner, D. Sharma, J. Nathans, D. J. Leah
Date :  30 Apr 01  (Deposition) - 11 Jul 01  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  D (1x),F (1x)
Biol. Unit 8:  B,E  (1x)
Biol. Unit 9:  A,C  (1x)
Biol. Unit 10:  D,F  (1x)
Keywords :  Wnt Receptor, Frizzled Protein Structure, Cysteine-Rich, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. E. Dann Iii, J. C. Hsieh, A. Rattner, D. Sharma, J. Nathans, D. J. Leahy
Insights Into Wnt Binding And Signalling From The Structure Of Two Frizzled Cysteine-Rich Domains.
Nature V. 412 86 2001
PubMed-ID: 11452312  |  Reference-DOI: 10.1038/35083601

(-) Compounds

Molecule 1 - SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System CellOVARY CELLS
    Expression System CommonCHINESE HAMSTER
    Expression System PlasmidPSGHV0
    Expression System Taxid10029
    Expression System Vector TypePLASMID
    FragmentCYSTEINE-RICH DOMAIN
    GeneSFRP-3
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A     
Biological Unit 2 (1x) B    
Biological Unit 3 (1x)  C   
Biological Unit 4 (1x)   D  
Biological Unit 5 (1x)    E 
Biological Unit 6 (1x)     F
Biological Unit 7 (1x)   D (1x) F (1x)
Biological Unit 8 (1x) B  E 
Biological Unit 9 (1x)A C   
Biological Unit 10 (1x)   D F

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 7 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 8 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 9 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 10 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:68 , GLN A:69 , HIS A:70 , GLU A:71 , ARG A:112 , HOH A:2380BINDING SITE FOR RESIDUE SO4 A 2336

(-) SS Bonds  (30, 30)

Asymmetric Unit
No.Residues
1A:3 -A:64
2A:11 -A:57
3A:48 -A:87
4A:76 -A:115
5A:80 -A:104
6B:3 -B:64
7B:11 -B:57
8B:48 -B:87
9B:76 -B:115
10B:80 -B:104
11C:3 -C:64
12C:11 -C:57
13C:48 -C:87
14C:76 -C:115
15C:80 -C:104
16D:3 -D:64
17D:11 -D:57
18D:48 -D:87
19D:76 -D:115
20D:80 -D:104
21E:3 -E:64
22E:11 -E:57
23E:48 -E:87
24E:76 -E:115
25E:80 -E:104
26F:3 -F:64
27F:11 -F:57
28F:48 -F:87
29F:76 -F:115
30F:80 -F:104

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Met A:21 -Pro A:22
2Met B:21 -Pro B:22
3Met C:21 -Pro C:22
4Met D:21 -Pro D:22
5Met E:21 -Pro E:22
6Met F:21 -Pro F:22

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IJX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IJX)

(-) Exons   (0, 0)

(no "Exon" information available for 1IJX)

(-) 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:125
 aligned with SFRP3_MOUSE | P97401 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:125
                                    42        52        62        72        82        92       102       112       122       132       142       152     
          SFRP3_MOUSE    33 AACEPVRIPLCKSLPWNMTKMPNHLHHSTQANAILAMEQFEGLLGTHCSPDLLFFLCAMYAPICTIDFQHEPIKPCKSVCERARQGCEPILIKYRHSWPESLACDELPVYDRGVCISPEAIVTAD 157
               SCOP domains d1ijxa_ A: Secreted Frizzled-related protein 3 (SFRP-3;fzb)                                                                   SCOP domains
               CATH domains 1ijxA00 A:1-125 Frizzled cysteine-rich domain                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..hhhhhhh...ee.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh....hhhhhhhhh......eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ijx A   1 AACEPVRIPLCKSLPWEMTKMPNHLHHSTQANAILAMEQFEGLLGTHCSPDLLFFLCAMYAPICTIDFQHEPIKPCKSVCERARQGCEPILIKYRHSWPESLACDELPVYDRGVCISPEAIVTAD 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with SFRP3_MOUSE | P97401 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:120
                                    42        52        62        72        82        92       102       112       122       132       142       152
          SFRP3_MOUSE    33 AACEPVRIPLCKSLPWNMTKMPNHLHHSTQANAILAMEQFEGLLGTHCSPDLLFFLCAMYAPICTIDFQHEPIKPCKSVCERARQGCEPILIKYRHSWPESLACDELPVYDRGVCISPEA 152
               SCOP domains d1ijxb_ B: Secreted Frizzled-related protein 3 (SFRP-3;fzb)                                                              SCOP domains
               CATH domains 1ijxB00 B:1-120 Frizzled cysteine-rich domain                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee..hhhhh.....ee.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh....hhhhhhhhh......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ijx B   1 AACEPVRIPLCKSLPWEMTKMPNHLHHSTQANAILAMEQFEGLLGTHCSPDLLFFLCAMYAPICTIDFQHEPIKPCKSVCERARQGCEPILIKYRHSWPESLACDELPVYDRGVCISPEA 120
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:125
 aligned with SFRP3_MOUSE | P97401 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:125
                                    42        52        62        72        82        92       102       112       122       132       142       152     
          SFRP3_MOUSE    33 AACEPVRIPLCKSLPWNMTKMPNHLHHSTQANAILAMEQFEGLLGTHCSPDLLFFLCAMYAPICTIDFQHEPIKPCKSVCERARQGCEPILIKYRHSWPESLACDELPVYDRGVCISPEAIVTAD 157
               SCOP domains d1ijxc_ C: Secreted Frizzled-related protein 3 (SFRP-3;fzb)                                                                   SCOP domains
               CATH domains 1ijxC00 C:1-125 Frizzled cysteine-rich domain                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..hhhhh.....ee.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh....hhhhh..........eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ijx C   1 AACEPVRIPLCKSLPWEMTKMPNHLHHSTQANAILAMEQFEGLLGTHCSPDLLFFLCAMYAPICTIDFQHEPIKPCKSVCERARQGCEPILIKYRHSWPESLACDELPVYDRGVCISPEAIVTAD 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     

Chain D from PDB  Type:PROTEIN  Length:122
 aligned with SFRP3_MOUSE | P97401 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:122
                                    43        53        63        73        83        93       103       113       123       133       143       153  
          SFRP3_MOUSE    34 ACEPVRIPLCKSLPWNMTKMPNHLHHSTQANAILAMEQFEGLLGTHCSPDLLFFLCAMYAPICTIDFQHEPIKPCKSVCERARQGCEPILIKYRHSWPESLACDELPVYDRGVCISPEAIVT 155
               SCOP domains d1ijxd_ D: Secreted Frizzled-related protein 3 (SFRP-3;fzb)                                                                SCOP domains
               CATH domains 1ijxD00 D:2-123 Frizzled cysteine-rich domain                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhh.....ee.........hhhhhhhhhh.hhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh....hhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ijx D   2 ACEPVRIPLCKSLPWEMTKMPNHLHHSTQANAILAMEQFEGLLGTHCSPDLLFFLCAMYAPICTIDFQHEPIKPCKSVCERARQGCEPILIKYRHSWPESLACDELPVYDRGVCISPEAIVT 123
                                    11        21        31        41        51        61        71        81        91       101       111       121  

Chain E from PDB  Type:PROTEIN  Length:123
 aligned with SFRP3_MOUSE | P97401 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:123
                                    43        53        63        73        83        93       103       113       123       133       143       153   
          SFRP3_MOUSE    34 ACEPVRIPLCKSLPWNMTKMPNHLHHSTQANAILAMEQFEGLLGTHCSPDLLFFLCAMYAPICTIDFQHEPIKPCKSVCERARQGCEPILIKYRHSWPESLACDELPVYDRGVCISPEAIVTA 156
               SCOP domains d1ijxe_ E: Secreted Frizzled-related protein 3 (SFRP-3;fzb)                                                                 SCOP domains
               CATH domains 1ijxE00 E:2-124 Frizzled cysteine-rich domain                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhhhh...ee.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh....hhhhhhhhh......eeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ijx E   2 ACEPVRIPLCKSLPWEMTKMPNHLHHSTQANAILAMEQFEGLLGTHCSPDLLFFLCAMYAPICTIDFQHEPIKPCKSVCERARQGCEPILIKYRHSWPESLACDELPVYDRGVCISPEAIVTA 124
                                    11        21        31        41        51        61        71        81        91       101       111       121   

Chain F from PDB  Type:PROTEIN  Length:125
 aligned with SFRP3_MOUSE | P97401 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:125
                                    42        52        62        72        82        92       102       112       122       132       142       152     
          SFRP3_MOUSE    33 AACEPVRIPLCKSLPWNMTKMPNHLHHSTQANAILAMEQFEGLLGTHCSPDLLFFLCAMYAPICTIDFQHEPIKPCKSVCERARQGCEPILIKYRHSWPESLACDELPVYDRGVCISPEAIVTAD 157
               SCOP domains d1ijxf_ F: Secreted Frizzled-related protein 3 (SFRP-3;fzb)                                                                   SCOP domains
               CATH domains 1ijxF00 F:1-125 Frizzled cysteine-rich domain                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..hhhhhhh...ee.........hhhhhhhhhh.hhhhhhh....hhhhhhhhhhh............eehhhhhhhhhhhhhhhhhhh....hhhhhhhhh.......ee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ijx F   1 AACEPVRIPLCKSLPWEMTKMPNHLHHSTQANAILAMEQFEGLLGTHCSPDLLFFLCAMYAPICTIDFQHEPIKPCKSVCERARQGCEPILIKYRHSWPESLACDELPVYDRGVCISPEAIVTAD 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     

   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, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IJX)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (SFRP3_MOUSE | P97401)
molecular function
    GO:0004930    G-protein coupled receptor activity    Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
    GO:0042813    Wnt-activated receptor activity    Combining with a Wnt protein and transmitting the signal across the plasma membrane to initiate a change in cell activity.
    GO:0017147    Wnt-protein binding    Interacting selectively and non-covalently with Wnt-protein, a secreted growth factor involved in signaling.
    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:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0090103    cochlea morphogenesis    The process in which the cochlea is generated and organized.
    GO:0060029    convergent extension involved in organogenesis    The morphogenetic process in which an epithelium narrows along one axis and lengthens in a perpendicular axis contribution to the shaping of an organ.
    GO:0042472    inner ear morphogenesis    The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
    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:0030178    negative regulation of Wnt signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway.
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0061037    negative regulation of cartilage development    Any process that decreases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0010721    negative regulation of cell development    Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0070367    negative regulation of hepatocyte differentiation    Any process that stops or decreases the rate or extent of hepatocyte differentiation.
    GO:0014033    neural crest cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neural crest cell.
    GO:0035567    non-canonical Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via effectors other than beta-catenin.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0045600    positive regulation of fat cell differentiation    Any process that activates or increases the frequency, rate or extent of adipocyte differentiation.
    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: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.

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  SFRP3_MOUSE | P97401
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1IJX)

(-) Related Entries Specified in the PDB File

1ijy CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MOUSE FRIZZLED 8 (MFZ8)