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- PDB-7vvg: Crystal Structure of HRasG12V(GMPPNP-bound) in complex with the R... -

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Basic information

Entry
Database: PDB / ID: 7vvg
TitleCrystal Structure of HRasG12V(GMPPNP-bound) in complex with the Ras-binding domain(RBD) of SIN1
Components
  • GTPase HRas
  • Target of rapamycin complex 2 subunit MAPKAP1
KeywordsCELL CYCLE / Ras / RBD
Function / homology
Function and homology information


TORC2 signaling / TORC2 complex / regulation of cellular response to oxidative stress / phosphatidic acid binding / negative regulation of Ras protein signal transduction / phospholipase C activator activity / serine/threonine protein kinase complex / GTPase complex / phosphatidylinositol-3,4-bisphosphate binding / oncogene-induced cell senescence ...TORC2 signaling / TORC2 complex / regulation of cellular response to oxidative stress / phosphatidic acid binding / negative regulation of Ras protein signal transduction / phospholipase C activator activity / serine/threonine protein kinase complex / GTPase complex / phosphatidylinositol-3,4-bisphosphate binding / oncogene-induced cell senescence / phosphatidylinositol-3,5-bisphosphate binding / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Constitutive Signaling by AKT1 E17K in Cancer / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / phosphatidylinositol-3,4,5-trisphosphate binding / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / CD28 dependent PI3K/Akt signaling / Activated NTRK2 signals through RAS / positive regulation of protein targeting to membrane / SHC1 events in ERBB4 signaling / adipose tissue development / enzyme-substrate adaptor activity / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / cellular response to nutrient levels / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / p38MAPK events / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / Signaling by FGFR2 in disease / phosphatidylinositol-4,5-bisphosphate binding / myelination / cytoskeleton organization / EPHB-mediated forward signaling / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / substantia nigra development / CD209 (DC-SIGN) signaling / intrinsic apoptotic signaling pathway / Downstream signal transduction / GRB2 events in ERBB2 signaling / negative regulation of insulin receptor signaling pathway / Insulin receptor signalling cascade / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / animal organ morphogenesis / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / small monomeric GTPase / VEGFR2 mediated vascular permeability / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / FCERI mediated MAPK activation / RAF activation / Signaling by ERBB2 TMD/JMD mutants / cellular response to gamma radiation / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / regulation of long-term neuronal synaptic plasticity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / small GTPase binding / positive regulation of type II interferon production / endocytosis
Similarity search - Function
Sin1, N-terminal / Stress-activated map kinase interacting protein 1 (SIN1) / TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases ...Sin1, N-terminal / Stress-activated map kinase interacting protein 1 (SIN1) / TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas / Target of rapamycin complex 2 subunit MAPKAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZheng, Y.Y. / Zhou, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
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
DepositionNov 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase HRas
C: Target of rapamycin complex 2 subunit MAPKAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2754
Polymers28,7282
Non-polymers5472
Water5,495305
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.032, 101.032, 124.208
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 18917.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112, small monomeric GTPase
#2: Protein Target of rapamycin complex 2 subunit MAPKAP1 / TORC2 subunit MAPKAP1 / Mitogen-activated protein kinase 2-associated protein 1 / Stress-activated ...TORC2 subunit MAPKAP1 / Mitogen-activated protein kinase 2-associated protein 1 / Stress-activated map kinase-interacting protein 1 / SAPK-interacting protein 1 / mSIN1


Mass: 9811.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAP1, MIP1, SIN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BPZ7
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 62.73 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→37.42 Å / Num. obs: 41729 / % possible obs: 99.92 % / Redundancy: 19.3 % / CC1/2: 1 / Rmerge(I) obs: 0.08135 / Net I/σ(I): 24.81
Reflection shellResolution: 1.7→1.761 Å / Rmerge(I) obs: 1.188 / Num. unique obs: 4102 / CC1/2: 0.893

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G0N

4g0n


Resolution: 1.7→37.42 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 3767 4.83 %
Rwork0.1778 74277 -
obs0.1789 41710 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.23 Å2 / Biso mean: 31.0448 Å2 / Biso min: 13.3 Å2
Refinement stepCycle: final / Resolution: 1.7→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 33 305 2280
Biso mean--18.54 40.8 -
Num. residues----243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.7-1.720.31781420.29142780
1.72-1.740.29361580.28652751
1.74-1.770.31221490.27292739
1.77-1.790.23321280.25532713
1.79-1.820.22341140.23362819
1.82-1.850.24621360.22512720
1.85-1.880.25061480.21972751
1.88-1.910.21581630.20832730
1.91-1.950.2321640.20392724
1.95-1.980.25651640.20372734
1.98-2.020.24841310.20292756
2.02-2.070.19181260.20172749
2.07-2.120.25961350.19332733
2.12-2.170.20991610.17982758
2.17-2.230.21451350.18232742
2.23-2.290.23591270.182785
2.29-2.370.19741400.17492724
2.37-2.450.17471450.17792750
2.45-2.550.20241700.18062716
2.55-2.670.20311170.17892786
2.67-2.810.20451360.18032770
2.81-2.980.15741050.17882769
2.98-3.210.14541460.16332734
3.21-3.540.2071340.15112764
3.54-4.050.19361340.14662769
4.05-5.10.16571280.1442751
5.1-37.420.20641310.18772760
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2993-0.132-0.21471.35770.30342.71580.21370.0281-0.00110.1497-0.1878-0.1786-0.34220.3605-0.05310.1688-0.0901-0.02250.23790.04830.1995-21.804234.374224.5017
28.1443-2.0174.30641.3781-1.15055.4946-0.2084-0.5040.49320.5419-0.0568-0.1129-0.4911-0.25830.19410.3149-0.1381-0.0090.24240.01190.2541-27.987138.893933.7533
37.275-2.224-0.63151.9173-0.02141.91520.0335-0.0550.06180.0273-0.0798-0.116-0.04380.33960.03230.1608-0.0892-0.01520.29230.05190.1862-17.913436.934321.6451
47.3122-5.4999-5.87567.27265.61397.97170.0517-0.3321-0.0519-0.0501-0.24230.8423-0.4373-0.69970.22230.3283-0.0437-0.05420.52030.01620.3114-34.003933.419414.9315
52.0621.2902-1.69912.5382-2.80544.7803-0.140.2303-0.2966-0.29390.11020.09110.4756-0.3246-0.03970.1835-0.0803-0.02330.1981-0.02090.218-31.019523.324121.1151
61.77281.12870.08573.2804-1.64010.8520.00280.0167-0.2948-0.0159-0.0509-0.03620.5786-0.06040.08870.1814-0.0853-0.03830.18070.02710.2264-25.900521.37727.5362
71.29350.6018-0.53232.4348-1.05662.62280.1169-0.1494-0.14470.057-0.2543-0.3190.17480.39840.04160.1364-0.0341-0.04630.2390.05490.2512-19.325421.757426.3366
84.8886-2.9301-1.87414.4226-1.00095.13550.09070.0005-0.05680.1528-0.07740.2101-0.1824-0.1192-0.03710.173-0.0656-0.00550.17780.01460.1696-31.0546.848420.2086
96.78012.1470.19742.55984.3329.7403-0.3574-0.1567-0.17650.7386-0.05351.0363-0.1986-0.10140.15630.25070.0160.10220.35290.04280.3647-42.199754.296225.2112
107.5587-5.23811.35073.9108-0.44844.171-0.2894-0.45660.05130.86680.1615-0.0151-0.0275-0.2110.15860.3414-0.09110.01520.31630.00720.2238-29.505251.901328.9989
111.26111.03340.3732.89510.63650.2575-0.0842-0.96380.29781.39450.44230.07650.02670.0443-0.09371.152-0.0753-0.13910.8238-0.10850.486-20.570155.372533.9471
124.85874.371-0.3327.1860.40925.91260.3344-0.11150.20820.2003-0.14140.05290.0594-0.0704-0.28370.3312-0.08590.00440.20490.00120.2161-25.359859.065122.0061
134.34241.7449-0.10232.97220.14191.39410.1142-0.16410.5078-0.010.03690.0366-0.35330.0845-0.18240.3647-0.063-0.00770.19810.01220.2615-29.961562.470919.5871
143.49320.7781-0.08331.93982.6347.4861-0.04820.00540.3396-0.1775-0.16470.652-0.2627-0.68570.06010.2673-0.0045-0.00240.26610.00650.3308-38.564257.90917.6482
156.59751.662-4.77545.9652.06276.02580.0179-0.1595-0.06980.5592-0.15-0.37880.17890.1084-0.10850.361-0.0896-0.06220.18310.04490.2339-24.80655.286920.7073
169.59135.33276.27924.09784.93116.0512-0.41930.2489-0.09320.68840.0895-0.4948-0.1711.51250.22970.3932-0.0142-0.0260.44460.06750.3387-17.946559.727621.4584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )A1 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 36 )A26 - 36
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 61 )A37 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 74 )A62 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 104 )A75 - 104
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 126 )A105 - 126
7X-RAY DIFFRACTION7chain 'A' and (resid 127 through 166 )A127 - 166
8X-RAY DIFFRACTION8chain 'C' and (resid 277 through 293 )C277 - 293
9X-RAY DIFFRACTION9chain 'C' and (resid 294 through 300 )C294 - 300
10X-RAY DIFFRACTION10chain 'C' and (resid 301 through 313 )C301 - 313
11X-RAY DIFFRACTION11chain 'C' and (resid 314 through 322 )C314 - 322
12X-RAY DIFFRACTION12chain 'C' and (resid 323 through 327 )C323 - 327
13X-RAY DIFFRACTION13chain 'C' and (resid 328 through 340 )C328 - 340
14X-RAY DIFFRACTION14chain 'C' and (resid 341 through 347 )C341 - 347
15X-RAY DIFFRACTION15chain 'C' and (resid 348 through 353 )C348 - 353
16X-RAY DIFFRACTION16chain 'C' and (resid 354 through 358 )C354 - 358

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