+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4727 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM Structure of the PI3-Kinase SH3 Domain Amyloid Fibril | |||||||||||||||
Map data | EM reconstruction of sh3 fibril, map sharpened with a B-factor of -150 A2 and low-pass filtered to 3.0 A. | |||||||||||||||
Sample |
| |||||||||||||||
Keywords | amyloid fibril / sh3 domain / PROTEIN FIBRIL | |||||||||||||||
Function / homology | Function and homology information RHOC GTPase cycle / PI3K events in ERBB4 signaling / Interleukin-7 signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / MET activates PI3K/AKT signaling / CDC42 GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle ...RHOC GTPase cycle / PI3K events in ERBB4 signaling / Interleukin-7 signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / MET activates PI3K/AKT signaling / CDC42 GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / FLT3 Signaling / RND2 GTPase cycle / RND1 GTPase cycle / IRS-mediated signalling / GPVI-mediated activation cascade / Signaling by SCF-KIT / Downstream signal transduction / PI3K/AKT activation / Signaling by ALK / Role of phospholipids in phagocytosis / Tie2 Signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Costimulation by the CD28 family / CD28 dependent PI3K/Akt signaling / RAC1 GTPase cycle / RAC2 GTPase cycle / Interleukin receptor SHC signaling / RND3 GTPase cycle / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / PI3K Cascade / PIP3 activates AKT signaling / GP1b-IX-V activation signalling / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Synthesis of PIPs at the plasma membrane / RHOA GTPase cycle / RHOF GTPase cycle / DAP12 signaling / RHOU GTPase cycle / RHOV GTPase cycle / Regulation of signaling by CBL / Downstream TCR signaling / RHOG GTPase cycle / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / phosphatidylinositol 3-kinase regulator activity / phosphatidylinositol 3-kinase activator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / ErbB-3 class receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / enzyme-substrate adaptor activity / Extra-nuclear estrogen signaling / G alpha (q) signalling events / intracellular glucose homeostasis / phosphatidylinositol phosphate biosynthetic process / insulin receptor substrate binding / phosphatidylinositol 3-kinase binding / insulin-like growth factor receptor binding / response to endoplasmic reticulum stress / phosphatidylinositol 3-kinase/protein kinase B signal transduction / substrate adhesion-dependent cell spreading / positive regulation of RNA splicing / insulin-like growth factor receptor signaling pathway / positive regulation of D-glucose import / positive regulation of protein localization to plasma membrane / insulin receptor binding / cellular response to insulin stimulus / positive regulation of protein import into nucleus / protein transport / insulin receptor signaling pathway / protein stabilization / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus Similarity search - Function | |||||||||||||||
Biological species | Bos taurus (cattle) | |||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
Authors | Roeder C / Vettore N | |||||||||||||||
Funding support | Germany, 4 items
| |||||||||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Atomic structure of PI3-kinase SH3 amyloid fibrils by cryo-electron microscopy. Authors: Christine Röder / Nicola Vettore / Lena N Mangels / Lothar Gremer / Raimond B G Ravelli / Dieter Willbold / Wolfgang Hoyer / Alexander K Buell / Gunnar F Schröder / Abstract: High resolution structural information on amyloid fibrils is crucial for the understanding of their formation mechanisms and for the rational design of amyloid inhibitors in the context of protein ...High resolution structural information on amyloid fibrils is crucial for the understanding of their formation mechanisms and for the rational design of amyloid inhibitors in the context of protein misfolding diseases. The Src-homology 3 domain of phosphatidyl-inositol-3-kinase (PI3K-SH3) is a model amyloid system that plays a pivotal role in our basic understanding of protein misfolding and aggregation. Here, we present the atomic model of the PI3K-SH3 amyloid fibril with a resolution determined to 3.4 Å by cryo-electron microscopy (cryo-EM). The fibril is composed of two intertwined protofilaments that create an interface spanning 13 residues from each monomer. The model comprises residues 1-77 out of 86 amino acids in total, with the missing residues located in the highly flexible C-terminus. The fibril structure allows us to rationalise the effects of chemically conservative point mutations as well as of the previously reported sequence perturbations on PI3K-SH3 fibril formation and growth. | |||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4727.map.gz | 38.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4727-v30.xml emd-4727.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4727_fsc.xml | 7.8 KB | Display | FSC data file |
Images | emd_4727.png | 252.9 KB | ||
Filedesc metadata | emd-4727.cif.gz | 5.9 KB | ||
Others | emd_4727_half_map_1.map.gz emd_4727_half_map_2.map.gz | 12.1 MB 10.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4727 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4727 | HTTPS FTP |
-Validation report
Summary document | emd_4727_validation.pdf.gz | 464.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4727_full_validation.pdf.gz | 464 KB | Display | |
Data in XML | emd_4727_validation.xml.gz | 13.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4727 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4727 | HTTPS FTP |
-Related structure data
Related structure data | 6r4rMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-11092 (Title: Micrographs of PI3-kinase SH3 amyloid fibrils / Data size: 32.0 Data #1: PI3-kinase SH3 amyloid fibrils, MotionCor2-aligned dose-weighted averages [micrographs - single frame] Data #2: PI3-kinase SH3 amyloid fibrils, MotionCor2-aligned non-dose-weighted averages [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_4727.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | EM reconstruction of sh3 fibril, map sharpened with a B-factor of -150 A2 and low-pass filtered to 3.0 A. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.935 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: #1
File | emd_4727_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_4727_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Fibril of PI3K-SH3 domains
Entire | Name: Fibril of PI3K-SH3 domains |
---|---|
Components |
|
-Supramolecule #1: Fibril of PI3K-SH3 domains
Supramolecule | Name: Fibril of PI3K-SH3 domains / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 34.55 kDa/nm |
-Macromolecule #1: Phosphatidylinositol 3-kinase regulatory subunit alpha
Macromolecule | Name: Phosphatidylinositol 3-kinase regulatory subunit alpha type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 9.649585 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: GSMSAEGYQY RALYDYKKER EEDIDLHLGD ILTVNKGSLV ALGFSDGQEA KPEEIGWLNG YNETTGERGD FPGTYVEYIG RKKISP UniProtKB: Phosphatidylinositol 3-kinase regulatory subunit alpha |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1.62 mg/mL |
---|---|
Buffer | pH: 2.5 / Component - Concentration: 0.11 mg/mL / Component - Formula: C2H6ClNO2 / Component - Name: glycin-hydrochloride |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 622 / Average exposure time: 65.0 sec. / Average electron dose: 26.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
---|---|
Output model | PDB-6r4r: |