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Yorodumi- PDB-5amo: Structure of a mouse Olfactomedin-1 disulfide-linked dimer of the... -
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-Basic information
Entry | Database: PDB / ID: 5amo | |||||||||
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Title | Structure of a mouse Olfactomedin-1 disulfide-linked dimer of the Olfactomedin domain and part of the coiled coil | |||||||||
Components | NOELIN | |||||||||
Keywords | SIGNALING PROTEIN / OLFM1 / DISULFIDE / NEUROBIOLOGY / DEVELOPMENT / AMPA RECEPTOR / BETA PROPELLER | |||||||||
Function / homology | Function and homology information extrinsic component of synaptic membrane / atrioventricular valve formation / neuronal signal transduction / 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 ...extrinsic component of synaptic membrane / atrioventricular valve formation / neuronal signal transduction / 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 / endoplasmic reticulum / signal transduction / extracellular space Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Pronker, M.F. / Bos, T.G.A.A. / Sharp, T.H. / Thies-Weesie, D.M. / Janssen, B.J.C. | |||||||||
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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5amo.cif.gz | 232 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5amo.ent.gz | 184.4 KB | Display | PDB format |
PDBx/mmJSON format | 5amo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5amo_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5amo_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5amo_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 5amo_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/5amo ftp://data.pdbj.org/pub/pdb/validation_reports/am/5amo | HTTPS FTP |
-Related structure data
Related structure data | 2940C 2941C 2942C 2943C 2944C 4d77S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54075.621 Da / Num. of mol.: 2 Fragment: COILED COIL AND OLFACTOMEDIN DOMAIN, RESIDUES 17-478 Source method: isolated from a genetically manipulated source Details: N-LINKED GLYCOSYLATION ON RESIDUES ASN473, ASN307 AND ASN394 Source: (gene. exp.) MUS MUSCULUS (house mouse) / Organ: BRAIN / Plasmid: PUPE107.03 / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: O88998 |
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-Sugars , 2 types, 6 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Sugar | |
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-Non-polymers , 3 types, 30 molecules
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | CORRESPOND |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: SITTING DROP AT 293 K, MIXING PROTEIN AT 6 MG/ML 1:1 WITH PRECIPITANT SOLUTION: 1M LICL, 20% PEG6000 (W/V) AND 100 MM TRIS PH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→95 Å / Num. obs: 26050 / % possible obs: 98.9 % / Observed criterion σ(I): -4 / Redundancy: 3.4 % / Biso Wilson estimate: 49.62 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.2 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4D77 Resolution: 2.4→50.318 Å / SU ML: 0.33 / σ(F): 1.92 / Phase error: 32.14 / Stereochemistry target values: ML Details: RESIDUES 17-210, 339-352 AND 478-487 NOT MODELED BECAUSE OF DISORDER OR LIMITED PROTEOLYSIS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.4242 Å2 / ksol: 1.3585 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50.318 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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