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- PDB-7vv8: Crystal Structure of HRasQ61L(GMPPNP-bound) in complex with the R... -

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Basic information

Entry
Database: PDB / ID: 7vv8
TitleCrystal Structure of HRasQ61L(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 / phosphatidylinositol-3,4-bisphosphate binding / phospholipase C activator activity / GTPase complex / positive regulation of ruffle assembly / 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 / phosphatidylinositol-3,4-bisphosphate binding / phospholipase C activator activity / GTPase complex / positive regulation of ruffle assembly / oncogene-induced cell senescence / phosphatidylinositol-3,5-bisphosphate binding / negative regulation of GTPase activity / enzyme-substrate adaptor activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / defense response to protozoan / Constitutive Signaling by AKT1 E17K in Cancer / phosphatidylinositol-3,4,5-trisphosphate binding / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / CD28 dependent PI3K/Akt signaling / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / positive regulation of protein targeting to membrane / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / adipose tissue development / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / cellular response to nutrient levels / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / membrane-membrane adaptor activity / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / cytoskeleton organization / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / phosphatidylinositol-4,5-bisphosphate binding / SHC1 events in EGFR signaling / substantia nigra development / EPHB-mediated forward signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / myelination / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / Downstream signal transduction / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / positive regulation of GTPase activity / positive regulation of MAP kinase activity / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of epithelial cell proliferation / small monomeric GTPase / VEGFR2 mediated cell proliferation / animal organ morphogenesis / 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 / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / cellular response to gamma radiation / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by SCF-KIT / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / small GTPase binding / cellular response to insulin stimulus
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 family 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 family 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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 4, 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)29,3054
Polymers28,7582
Non-polymers5472
Water5,026279
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)101.316, 101.316, 124.291
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

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


Mass: 18947.297 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.: 279 / 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: 3.2 Å3/Da / Density % sol: 61.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG20000, 0.1M Sodim citrate. pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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

4g0n


Resolution: 1.7→26.49 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / Phase error: 18.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 3746 4.82 %
Rwork0.1796 73910 -
obs-41497 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.43 Å2 / Biso mean: 27.1099 Å2 / Biso min: 8.19 Å2
Refinement stepCycle: final / Resolution: 1.7→26.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 33 279 2260
Biso mean--13.7 37.86 -
Num. residues----245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.720.22611460.22532760100
1.72-1.740.25431520.21482726100
1.74-1.770.23191480.22022740100
1.77-1.790.23221290.2062275699
1.79-1.820.2071160.2052275199
1.82-1.850.26421170.2131274498
1.85-1.880.23661630.2038271699
1.88-1.910.2181520.185277099
1.91-1.950.22151620.1785271599
1.95-1.980.19951760.18022729100
1.98-2.020.22551210.17372771100
2.02-2.070.18291400.17182802100
2.07-2.120.22031250.17572745100
2.12-2.170.20481610.1742747100
2.17-2.230.24331390.17332752100
2.23-2.290.21911270.17212815100
2.29-2.370.16181450.17532730100
2.37-2.450.17521500.17792759100
2.45-2.550.19091680.18322734100
2.55-2.670.22331170.17182788100
2.67-2.810.18781420.18342752100
2.81-2.980.16831020.18112813100
2.98-3.210.17461430.1717271799
3.21-3.530.181340.165269397
3.53-4.040.17621250.1548266896
4.04-5.090.18941240.1489260594
5.09-26.490.20991220.1872261293
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)
15.68491.5865-2.32481.2164-1.03081.54610.14180.12340.1954-0.0378-0.0188-0.132-0.18150.3102-0.03710.1109-0.08150.00770.26460.02650.1652-18.154234.16117.2213
20.87740.22470.1040.29-0.07370.06320.1089-0.16380.20270.241-0.15010.0542-0.1720.0564-0.06960.159-0.2466-0.00450.21280.05130.1522-26.040436.777131.8865
33.4395-0.476-0.12070.60220.10190.47040.0188-0.01630.01760.0128-0.0807-0.0162-0.01380.29420.02840.1308-0.1016-0.01230.32810.04820.1639-17.74736.979221.6062
45.913-2.1759-3.5951.60591.5914.02550.0576-0.05760.1394-0.0315-0.07430.2846-0.1486-0.3007-0.00390.2547-0.0903-0.03550.41550.03020.2081-33.961933.820215.0015
50.72810.2696-0.94730.7085-0.98082.1279-0.04880.2617-0.1986-0.20310.04660.08750.2645-0.26890.01430.1747-0.1177-0.03150.2030.00230.1759-30.978423.515420.8484
60.6456-0.1877-1.53661.76883.26688.9154-0.00590.1371-0.1472-0.341-0.0494-0.0379-0.40650.09130.05990.1874-0.0628-0.01010.18650.01250.1554-23.652722.181617.4885
70.56440.02630.09020.85930.06510.76260.1594-0.1287-0.14240.214-0.1428-0.17960.19530.2954-0.01930.1516-0.0769-0.05160.20860.04970.1902-21.040321.412128.3774
84.9997-0.3528-0.95280.8113-0.11451.80530.00220.0641-0.18760.04830.00770.23630.102-0.22040.0070.1627-0.0875-0.03010.17190.02930.1819-33.670747.360218.9692
93.9519-0.2478-0.91841.82190.19161.53830.0476-0.17770.01360.14620.0125-0.0456-0.1156-0.0089-0.04810.1365-0.1028-0.00840.16610.02650.1489-28.899246.779822.3788
104.54052.23370.77182.21642.16843.27140.0009-0.12910.00940.1587-0.02280.1496-0.0816-0.2204-0.01860.2941-0.00830.09090.39210.00330.3281-42.539755.179125.6018
112.3256-1.39450.30973.5552-0.01882.191-0.0518-0.2863-0.00290.380.11110.0921-0.0187-0.0724-0.02290.3106-0.09520.01540.30420.00830.1542-29.456251.989629.1475
122.0831-0.46540.11162.0844-0.41062.1732-0.026-0.29370.02620.33720.1392-0.1798-0.03590.1249-0.01150.4178-0.1244-0.05510.24030.00830.1822-23.483657.797226.7733
132.26380.6615-0.45861.24880.07341.28230.0541-0.0850.25040.06630.00830.0507-0.2027-0.0382-0.08540.3868-0.0651-00.19240.00440.2245-29.949762.634719.7597
140.1504-0.5265-0.59936.26071.47713.78240.00960.01310.1660.0035-0.03870.2812-0.2048-0.2969-0.00370.2333-0.0099-0.00790.2347-0.00180.2392-38.582458.065917.8323
151.28731.844-0.42595.11951.54824.40350.09050.0592-0.24410.17870.0232-0.30110.00740.2398-0.13030.3054-0.0921-0.0320.18730.01330.1717-24.70955.414120.6323
163.69343.18073.86852.74973.33414.0520.00610.0592-0.01380.11610.0574-0.1528-0.05240.3382-0.10950.3106-0.0431-0.03980.3510.04690.3072-17.924759.906221.6258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 36 )A11 - 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 116 )A105 - 116
7X-RAY DIFFRACTION7chain 'A' and (resid 117 through 166 )A117 - 166
8X-RAY DIFFRACTION8chain 'C' and (resid 277 through 285 )C277 - 285
9X-RAY DIFFRACTION9chain 'C' and (resid 286 through 294 )C286 - 294
10X-RAY DIFFRACTION10chain 'C' and (resid 295 through 300 )C295 - 300
11X-RAY DIFFRACTION11chain 'C' and (resid 301 through 313 )C301 - 313
12X-RAY DIFFRACTION12chain 'C' and (resid 314 through 327 )C314 - 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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