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- EMDB-1223: The dynamics of signal triggering in a gp130-receptor complex. -

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Basic information

Entry
Database: EMDB / ID: EMD-1223
TitleThe dynamics of signal triggering in a gp130-receptor complex.
Map dataThis is a cEM map of the extracellular portion of the IL11 hexameric complex
Sample
  • Sample: IL11-IL11-R-gp130
  • Protein or peptide: Interleukin-11
  • Protein or peptide: Interleukin-11 Receptor
  • Protein or peptide: Glycoprotein 130
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 30.0 Å
AuthorsMatadeen R / Hon W / Jones EY / Fuller S
CitationJournal: Structure / Year: 2007
Title: The dynamics of signal triggering in a gp130-receptor complex.
Authors: Rishi Matadeen / Wai-Ching Hon / John K Heath / E Yvonne Jones / Stephen Fuller /
Abstract: gp130 is a shared signal-transducing membrane-associated receptor for several hematopoietic cytokines. The 30 A resolution cryo-electron microscopy (cryo-EM) structure of the Interleukin 11(IL-11)-IL- ...gp130 is a shared signal-transducing membrane-associated receptor for several hematopoietic cytokines. The 30 A resolution cryo-electron microscopy (cryo-EM) structure of the Interleukin 11(IL-11)-IL-11 Receptor-gp130 extracellular complex reveals the architecture and dynamics of this gp130-containing signaling complex. Normal-mode analysis reveals a repertoire of conformational changes that could function in signal triggering. This suggests a concerted mechanism of signaling involving all the components of the complex. This could provide a general mechanism of signal transfer for cytokines utilizing the JAK-STAT signaling cascade.
History
DepositionMay 10, 2006-
Header (metadata) releaseMay 10, 2006-
Map releaseMay 2, 2007-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.212920934
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.213
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1223.gif

Downloads & links

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Map

FileDownload / File: emd_1223.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a cEM map of the extracellular portion of the IL11 hexameric complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.3 Å/pix.
x 80 pix.
= 264. Å		3.3 Å/pix.
x 80 pix.
= 264. Å		3.3 Å/pix.
x 80 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.3 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.225 / Movie #1: 0.2129209
Minimum - Maximum-0.906879 - 0.948235
Average (Standard dev.)0.00765807 (±0.0871348)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 264 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.33.33.3
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.9070.9480.008

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Supplemental data

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Sample components

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Entire : IL11-IL11-R-gp130

EntireName: IL11-IL11-R-gp130
Components
  • Sample: IL11-IL11-R-gp130
  • Protein or peptide: Interleukin-11
  • Protein or peptide: Interleukin-11 Receptor
  • Protein or peptide: Glycoprotein 130

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Supramolecule #1000: IL11-IL11-R-gp130

SupramoleculeName: IL11-IL11-R-gp130 / type: sample / ID: 1000 / Oligomeric state: hexamer / Number unique components: 3
Molecular weightTheoretical: 270 KDa

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Macromolecule #1: Interleukin-11

MacromoleculeName: Interleukin-11 / type: protein_or_peptide / ID: 1 / Name.synonym: IL-11 / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House Mouse
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET15b

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Macromolecule #2: Interleukin-11 Receptor

MacromoleculeName: Interleukin-11 Receptor / type: protein_or_peptide / ID: 2 / Name.synonym: IL-11R / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House mouse
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)

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Macromolecule #3: Glycoprotein 130

MacromoleculeName: Glycoprotein 130 / type: protein_or_peptide / ID: 3 / Name.synonym: gp130 / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House Mouse
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Details: 5mM HEPES 100mM NaCl 1mM DTT 0.25% B-octylglucopyranoside
GridDetails: 300 mesh holy carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Image recordingCategory: CCD / Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 8.3 µm / Number real images: 15 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50100 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: Imagic / Number images used: 830
Final two d classificationNumber classes: 100

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Atomic model buiding 1

SoftwareName: URO
DetailsProtocol: Rigid Body
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT

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