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- EMDB-2940: Structural characterization of the Olfactomedin-1 disulfide-linke... -

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Basic information

Entry
Database: EMDB / ID: EMD-2940
TitleStructural characterization of the Olfactomedin-1 disulfide-linked tetramer
Map dataFiltered subtomogram of Olfactomedin-1 tetramer
Sample
  • Sample: Olfactomedin-1 disulfide-linked tetramer
  • Organelle or cellular component: Olfactomedin-1
KeywordsOlfactomedin-1 (Olfm1) / neurobiology / tetramer / X-ray crystallography / small-angle X-ray scattering (SAXS) / electron tomography / analytical ultracentrifugation (AUC) / coiled coil / calcium / disulfide
Biological speciesMus musculus (house mouse)
Methodelectron tomography / negative staining
AuthorsSharp TH / Pronker MF / Bos TG / Thies-Weesie DM / Janssen BJC
CitationJournal: 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
DepositionMar 18, 2015-
Header (metadata) releaseApr 1, 2015-
Map releaseNov 18, 2015-
UpdateNov 25, 2015-
Current statusNov 25, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_2940.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFiltered subtomogram of Olfactomedin-1 tetramer
Voxel sizeX=Y=Z: 4.57 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-4.06473494 - 5.96464968
Average (Standard dev.)0.00889589 (±0.22364238)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 457.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.574.574.57
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z457.000457.000457.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-4.0655.9650.009

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Supplemental data

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Sample components

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Entire : Olfactomedin-1 disulfide-linked tetramer

EntireName: Olfactomedin-1 disulfide-linked tetramer
Components
  • Sample: Olfactomedin-1 disulfide-linked tetramer
  • Organelle or cellular component: Olfactomedin-1

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Supramolecule #1000: Olfactomedin-1 disulfide-linked tetramer

SupramoleculeName: Olfactomedin-1 disulfide-linked tetramer / type: sample / ID: 1000 / Oligomeric state: Tetramer / Number unique components: 1
Molecular weightExperimental: 242 KDa / Theoretical: 256 KDa / Method: AUC

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Supramolecule #1: Olfactomedin-1

SupramoleculeName: 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
Ref INTERPROdivclassse 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 INTERPROdivclassse 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 weightExperimental: 242 KDa / Theoretical: 256 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293ES / Recombinant plasmid: pUPE107.03

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Experimental details

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Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

Concentration0.065 mg/mL
BufferpH: 7.5 / Details: 150 mM NaCl, 20 mM HEPES
StainingType: 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.
GridDetails: Carbon-coated mesh copper grids glow discharged for 15 sec
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 30000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -58 ° / Tilt series - Axis1 - Max angle: 58 ° / Tilt series - Axis1 - Angle increment: 2 °
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 30,000 times magnification
DetailsWeak beam illumination
DateFeb 12, 2015
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 58 / Bits/pixel: 32
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: IMOD, each tilt image
Final reconstructionAlgorithm: 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
DetailsTilt 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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Atomic model buiding 1

Initial modelPDB ID:

Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: Chimera
DetailsEach coiled-coil dimer of the tetramer was fitted as a rigid body.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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