+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDAS7 |
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Sample | mouse olfactomedin-1
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Function / homology | Function and homology information extrinsic component of synaptic membrane / atrioventricular valve formation / neuronal signal transduction / extrinsic component of postsynaptic density membrane / cardiac epithelial to mesenchymal transition / regulation of axon extension / AMPA glutamate receptor complex / axonal growth cone / positive regulation of epithelial to mesenchymal transition / synaptic membrane ...extrinsic component of synaptic membrane / atrioventricular valve formation / neuronal signal transduction / extrinsic component of postsynaptic density membrane / cardiac epithelial to mesenchymal transition / regulation of axon extension / AMPA glutamate receptor complex / axonal growth cone / positive regulation of epithelial to mesenchymal transition / synaptic membrane / perikaryon / positive regulation of apoptotic process / axon / negative regulation of gene expression / neuronal cell body / glutamatergic synapse / positive regulation of gene expression / signal transduction / endoplasmic reticulum / extracellular space Similarity search - Function |
Biological species | Mus musculus (house mouse) |
Citation | Journal: J Biol Chem / Year: 2015 Title: Olfactomedin-1 Has a V-shaped Disulfide-linked Tetrameric Structure. Authors: Matti F Pronker / Trusanne G A A Bos / Thomas H Sharp / Dominique M E Thies-Weesie / Bert J C Janssen / Abstract: Olfactomedin-1 (Olfm1; also known as noelin and pancortin) is a member of the olfactomedin domain-containing superfamily and a highly expressed neuronal glycoprotein important for nervous system ...Olfactomedin-1 (Olfm1; also known as noelin and pancortin) is a member of the olfactomedin domain-containing superfamily and a highly expressed neuronal glycoprotein important for nervous system development. It binds a number of secreted proteins and cell surface-bound receptors to induce cell signaling processes. Using a combined approach of x-ray crystallography, solution scattering, analytical ultracentrifugation, and electron microscopy we determined that full-length Olfm1 forms disulfide-linked tetramers with a distinctive V-shaped architecture. The base of the "V" is formed by two disulfide-linked dimeric N-terminal domains. Each of the two V legs consists of a parallel dimeric disulfide-linked coiled coil with a C-terminal β-propeller dimer at the tips. This agrees with our crystal structure of a C-terminal coiled-coil segment and β-propeller combination (Olfm1(coil-Olf)) that reveals a disulfide-linked dimeric arrangement with the β-propeller top faces in an outward exposed orientation. Similar to its family member myocilin, Olfm1 is stabilized by calcium. The dimer-of-dimers architecture suggests a role for Olfm1 in clustering receptors to regulate signaling and sheds light on the conformation of several other olfactomedin domain family members. |
Contact author |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDAS7 |
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-Related structure data
Related structure data | 2940C 2941C 2942C 2943C 2944C 5amoC C: citing same article (ref.) |
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Similar structure data |
-External links
Related items in Molecule of the Month |
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-Models
Model #298 | Type: dummy / Software: Dammif / Radius of dummy atoms: 6.30 A / Chi-square value: 4.313 Search similar-shape structures of this assembly by Omokage search (details) |
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-Sample
Sample | Name: mouse olfactomedin-1 / Specimen concentration: 3.55 mg/ml |
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Buffer | Name: 20 mM HEPES 150 mM NaCl / Concentration: 20.00 mM / pH: 7.5 / Composition: 150 mM NaCl |
Entity #163 | Name: Olfactomedin-1 / Type: protein / Description: Noelin / Formula weight: 64 / Num. of mol.: 4 / Source: Mus musculus / References: UniProt: O88998 Sequence: MITNWMSQTL PSLVGLNTTR LSAASGGTLD RSTGVLPTNP EESWQVYSSA QDSEGRCICT VVAPQQTMCS RDARTKQLRQ LLEKVQNMSQ SIEVLDRRTQ RDLQYVEKME NQMKGLETKF KQVEESHKQH LARQFKAIKA KMDELRPLIP VLEEYKADAK LVLQFKEEVQ ...Sequence: MITNWMSQTL PSLVGLNTTR LSAASGGTLD RSTGVLPTNP EESWQVYSSA QDSEGRCICT VVAPQQTMCS RDARTKQLRQ LLEKVQNMSQ SIEVLDRRTQ RDLQYVEKME NQMKGLETKF KQVEESHKQH LARQFKAIKA KMDELRPLIP VLEEYKADAK LVLQFKEEVQ NLTSVLNELQ EEIGAYDYDE LQSRVSNLEE RLRACMQKLA CGKLTGISDP VTVKTSGSRF GSWMTDPLAP EGDNRVWYMD GYHNNRFVRE YKSMVDFMNT DNFTSHRLPH PWSGTGQVVY NGSIYFNKFQ SHIIIRFDLK TETILKTRSL DYAGYNNMYH YAWGGHSDID LMVDENGLWA VYATNQNAGN IVISKLDPVS LQILQTWNTS YPKRSAGEAF IICGTLYVTN GYSGGTKVHY AYQTNASTYE YIDIPFQNKY SHISMLDYNP KDRALYAW |
-Experimental information
Beam | Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.93 Å / Dist. spec. to detc.: 2.43 mm | ||||||||||||||||||||||||
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Detector | Name: Pilatus 1M | ||||||||||||||||||||||||
Scan | Title: mouse Olfactomedin-1 / Measurement date: Nov 6, 2013 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 0.056 sec. / Number of frames: 18 / Unit: 1/nm /
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Distance distribution function P(R) | Sofotware P(R): GNOM 4.5a / Number of points: 205 /
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Result | D max: 30 / Type of curve: single_conc Comments: SAXS was used to determine that Olfactomedin-1 forms tetramers in solution (confirmed by SEC-MALS and AUC). Scattering data were combined with crystallographic and negative stain electron ...Comments: SAXS was used to determine that Olfactomedin-1 forms tetramers in solution (confirmed by SEC-MALS and AUC). Scattering data were combined with crystallographic and negative stain electron tomography data to construct a model of a V-shaped dimer-of-dimers.
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