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- PDB-7vv8: Crystal Structure of HRasQ61L(GMPPNP-bound) in complex with the R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vv8 | ||||||
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Title | Crystal Structure of HRasQ61L(GMPPNP-bound) in complex with the Ras-binding domain(RBD) of SIN1 | ||||||
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![]() | CELL CYCLE / Ras / RBD | ||||||
Function / homology | ![]() TORC2 signaling / TORC2 complex / regulation of cellular response to oxidative stress / phosphatidic acid binding / phosphatidylinositol-3,4-bisphosphate binding / negative regulation of Ras protein signal transduction / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / phosphatidylinositol-3,5-bisphosphate binding ...TORC2 signaling / TORC2 complex / regulation of cellular response to oxidative stress / phosphatidic acid binding / phosphatidylinositol-3,4-bisphosphate binding / negative regulation of Ras protein signal transduction / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / phosphatidylinositol-3,5-bisphosphate binding / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Constitutive Signaling by AKT1 E17K in Cancer / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / CD28 dependent PI3K/Akt signaling / phosphatidylinositol-3,4,5-trisphosphate binding / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / EGFR Transactivation by Gastrin / SHC1 events in EGFR signaling / positive regulation of protein targeting to membrane / Signalling to RAS / GRB2 events in ERBB2 signaling / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / cellular response to nutrient levels / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC1 events in ERBB2 signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Schwann cell development / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / positive regulation of epithelial cell proliferation / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / cytoskeleton organization / Signaling by FGFR2 in disease / phosphatidylinositol-4,5-bisphosphate binding / EPHB-mediated forward signaling / Signaling by FLT3 fusion proteins / substantia nigra development / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / myelination / Signaling by FGFR1 in disease / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / Signaling by ERBB2 TMD/JMD mutants / small monomeric GTPase / positive regulation of MAP kinase activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated vascular permeability / G protein activity / positive regulation of GTPase activity / VEGFR2 mediated cell proliferation / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / positive regulation of JNK cascade / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Signaling by SCF-KIT / cellular senescence / cellular response to gamma radiation / small GTPase binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zheng, Y.Y. / Zhou, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into Ras regulation by SIN1. Authors: Zheng, Y. / Ding, L. / Meng, X. / Potter, M. / Kearney, A.L. / Zhang, J. / Sun, J. / James, D.E. / Yang, G. / Zhou, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.4 KB | Display | ![]() |
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PDB format | ![]() | 94.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7vv9C ![]() 7vvbC ![]() 7vvgC ![]() 4g0nS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18947.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 9811.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-GNP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG20000, 0.1M Sodim citrate. pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→26.49 Å / Num. obs: 41520 / % possible obs: 98.87 % / Redundancy: 16.5 % / Biso Wilson estimate: 19.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07592 / Net I/σ(I): 25.57 |
Reflection shell | Resolution: 1.7→1.761 Å / Rmerge(I) obs: 0.7526 / Num. unique obs: 4098 / CC1/2: 0.897 / % possible all: 99.78 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4G0N Resolution: 1.7→26.49 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / Phase error: 18.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.43 Å2 / Biso mean: 27.1099 Å2 / Biso min: 8.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→26.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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