+Open data
-Basic information
Entry | Database: PDB / ID: 6r4r | |||||||||||||||
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Title | Cryo-EM Structure of the PI3-Kinase SH3 Domain Amyloid Fibril | |||||||||||||||
Components | Phosphatidylinositol 3-kinase regulatory subunit alpha | |||||||||||||||
Keywords | PROTEIN FIBRIL / amyloid fibril / sh3 domain | |||||||||||||||
Function / homology | Function and homology information Signaling by ALK / MET activates PI3K/AKT signaling / RHOC GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / RAC2 GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle / FLT3 Signaling ...Signaling by ALK / MET activates PI3K/AKT signaling / RHOC GTPase cycle / CDC42 GTPase cycle / RAC1 GTPase cycle / RAC2 GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle / FLT3 Signaling / RND3 GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / PI3K events in ERBB4 signaling / Interleukin-7 signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / IRS-mediated signalling / GPVI-mediated activation cascade / Signaling by SCF-KIT / Downstream signal transduction / PI3K/AKT activation / 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 / RAF/MAP kinase cascade / Interleukin receptor SHC signaling / 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 / 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 / ErbB-3 class receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / positive regulation of endoplasmic reticulum unfolded protein response / phosphatidylinositol 3-kinase complex, class IA / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex / Extra-nuclear estrogen signaling / G alpha (q) signalling events / intracellular glucose homeostasis / phosphatidylinositol phosphate biosynthetic process / insulin receptor substrate binding / phosphatidylinositol 3-kinase binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to endoplasmic reticulum stress / substrate adhesion-dependent cell spreading / insulin-like growth factor receptor signaling pathway / positive regulation of RNA splicing / positive regulation of glucose import / positive regulation of protein localization to plasma membrane / insulin-like growth factor receptor binding / insulin receptor binding / positive regulation of protein import into nucleus / cellular response to insulin stimulus / 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 | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
Authors | Roeder, C. / Vettore, N. / Mangels, L.N. / Gremer, L. / Ravelli, R.B.G. / Willbold, D. / Hoyer, W. / Buell, A.K. / Schroder, G.F. | |||||||||||||||
Funding support | Germany, 4items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6r4r.cif.gz | 103 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r4r.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 6r4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/6r4r ftp://data.pdbj.org/pub/pdb/validation_reports/r4/6r4r | HTTPS FTP |
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-Related structure data
Related structure data | 4727MC M: map data used to model this data C: citing same article (ref.) |
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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
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 9649.585 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: PIK3R1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P23727 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Fibril of PI3K-SH3 domains / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 34.55 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Bos taurus (cattle) |
Source (recombinant) | Organism: Escherichia coli BL21 (bacteria) |
Buffer solution | pH: 2.5 |
Buffer component | Conc.: 0.11 mg/mL / Name: glycin-hydrochloride / Formula: C2H6ClNO2 |
Specimen | Conc.: 1.62 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Image recording | Average exposure time: 65 sec. / Electron dose: 26 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 622 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 179.436 ° / Axial rise/subunit: 2.3548 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 103733 / Details: Filaments were picked manually in Relion2 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27681 Details: For the even/odd test, the segment images were split by entire fibrils and refined separately for 25 iterations using the same reference density (low-passed filtered to 20 A). Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |