SASDAS7: mouse olfactomedin-1 (Noelin, Olfactomedin-1)

Basic information

• Entry: Database: SASBDB / ID: SASDAS7

Sample

mouse olfactomedin-1

• Noelin (protein), Olfactomedin-1, Mus musculus

Function / homology

Function:

extrinsic component of synaptic membrane / atrioventricular valve formation / neuronal signal transduction / cardiac epithelial to mesenchymal transition / regulation of axon extension / AMPA glutamate receptor complex / positive regulation of epithelial to mesenchymal transition / axonal growth cone / synaptic membrane / perikaryon / positive regulation of apoptotic process / axon / negative regulation of gene expression / neuronal cell body / glutamatergic synapse / positive regulation of gene expression / endoplasmic reticulum / signal transduction / extracellular space

Domain/homology:

Noelin domain / Neurogenesis glycoprotein / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / Quinoprotein amine dehydrogenase, beta chain-like / Endoplasmic reticulum targeting sequence.

Component:

Noelin

• 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 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

• Matti Pronker (Utrecht University, Utrecht, Netherlands)

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)

Sample

• Sample: Name: mouse olfactomedin-1 / Specimen concentration: 3.55 mg/ml
• 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 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 synchrotronSynchrotron / Wavelength: 0.93 Å / Dist. spec. to detc.: 2.43 mm
• 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 /

	Min	Max
Q	0.028	4.4936

Distance distribution function P(R)

Sofotware P(R): GNOM 4.5a / Number of points: 205 /

	Min	Max
Q	0.05819	0.9375
P(R) point	8	212
R	0	29.86

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 tomography data to construct a model of a V-shaped dimer-of-dimers.

	Experimental	Porod
MW	249 kDa	323 kDa
Volume	-	616 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	250.9	0.2	249	0.3
Radius of gyration, Rg	8.79 nm	0.008	8.5 nm	-