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Yorodumi- EMDB-2940: Structural characterization of the Olfactomedin-1 disulfide-linke... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2940 | |||||||||
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Title | Structural characterization of the Olfactomedin-1 disulfide-linked tetramer | |||||||||
Map data | Filtered subtomogram of Olfactomedin-1 tetramer | |||||||||
Sample |
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Keywords | Olfactomedin-1 (Olfm1) / neurobiology / tetramer / X-ray crystallography / small-angle X-ray scattering (SAXS) / electron tomography / analytical ultracentrifugation (AUC) / coiled coil / calcium / disulfide | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | electron tomography / negative staining | |||||||||
Authors | Sharp TH / Pronker MF / Bos TG / Thies-Weesie DM / Janssen BJC | |||||||||
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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2940.map.gz | 377.1 KB | EMDB map data format | |
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Header (meta data) | emd-2940-v30.xml emd-2940.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | 2940.png | 67.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2940 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2940 | HTTPS FTP |
-Validation report
Summary document | emd_2940_validation.pdf.gz | 128.6 KB | Display | EMDB validaton report |
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Full document | emd_2940_full_validation.pdf.gz | 127.7 KB | Display | |
Data in XML | emd_2940_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2940 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2940 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2940.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Filtered subtomogram of Olfactomedin-1 tetramer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.57 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Olfactomedin-1 disulfide-linked tetramer
Entire | Name: Olfactomedin-1 disulfide-linked tetramer |
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Components |
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-Supramolecule #1000: Olfactomedin-1 disulfide-linked tetramer
Supramolecule | Name: Olfactomedin-1 disulfide-linked tetramer / type: sample / ID: 1000 / Oligomeric state: Tetramer / Number unique components: 1 |
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Molecular weight | Experimental: 242 KDa / Theoretical: 256 KDa / Method: AUC |
-Supramolecule #1: Olfactomedin-1
Supramolecule | Name: Olfactomedin-1 / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Olfm1, noelin, pancortin Details: Purified recombinant full-length glycoslated Olfactomedin-1 tetramers were negatively stained with uranyl formate. Number of copies: 1 / Oligomeric state: Tetramer / Recombinant expression: Yes |
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Ref INTERPRO | divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp ... divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp kIPR022082 ampajax1cl asspoptrgi IPR022082i spandiv |
Ref INTERPRO | divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp ... divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp kIPR003112 ampajax1cl asspoptrgi IPR003112i spandiv |
Source (natural) | Organism: Mus musculus (house mouse) / synonym: House Mouse / Tissue: brain / Cell: neuron / Organelle: Secretory pathway / Location in cell: Secreted (ER/golgi/extracellular) |
Molecular weight | Experimental: 242 KDa / Theoretical: 256 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293ES / Recombinant plasmid: pUPE107.03 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Concentration | 0.065 mg/mL |
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Buffer | pH: 7.5 / Details: 150 mM NaCl, 20 mM HEPES |
Staining | Type: NEGATIVE Details: Full-length Olfm1 was adsorbed to grids for 30 sec. Grids were briefly washed with water and then stained for 30 sec with a freshly prepared filtered 2% uranyl formate solution. |
Grid | Details: Carbon-coated mesh copper grids glow discharged for 15 sec |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 30,000 times magnification |
Details | Weak beam illumination |
Date | Feb 12, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 58 / Bits/pixel: 32 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 30000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -58 ° / Tilt series - Axis1 - Max angle: 58 ° / Tilt series - Axis1 - Angle increment: 2 ° |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Tilt series were collected from -58 to 58 degrees in 2 degree increments. The first and last image was discarded. CTF correction was performed on each projection |
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Final reconstruction | Algorithm: OTHER / Software - Name: IMOD, EMAN2 Details: Sub-tomogram particles were manually picked using e2spt_boxer.py from EMAN2. Each particle was normalized and masked with a sharp spherical mask to remove background density not associated ...Details: Sub-tomogram particles were manually picked using e2spt_boxer.py from EMAN2. Each particle was normalized and masked with a sharp spherical mask to remove background density not associated with the protein. Particles were then filtered to 20 A with a low-pass Gaussian filter, before a tight mask was applied to the remaining density using e2proc3d.py from EMAN2. Number images used: 57 |
CTF correction | Details: IMOD, each tilt image |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: Chimera |
Details | Each coiled-coil dimer of the tetramer was fitted as a rigid body. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |