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- PDB-7vv9: Crystal Structure of HRas(GMPPNP-bound) in complex with the Ras-b... -

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Basic information

Entry
Database: PDB / ID: 7vv9
TitleCrystal Structure of HRas(GMPPNP-bound) in complex with the Ras-binding domain(RBD) of SIN1
Components
  • GTPase HRasHRAS
  • 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 / GTPase complex / phosphatidylinositol-3,5-bisphosphate binding / oncogene-induced cell senescence / positive regulation of ruffle assembly ...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 / GTPase complex / phosphatidylinositol-3,5-bisphosphate binding / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / 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 / cellular response to nutrient levels / CD28 dependent PI3K/Akt signaling / phosphatidylinositol-3,4,5-trisphosphate binding / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / cytoskeleton organization / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / phosphatidylinositol-4,5-bisphosphate binding / EGFR Transactivation by Gastrin / substantia nigra development / myelination / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / small monomeric GTPase / G protein activity / VEGFR2 mediated vascular permeability / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / cellular response to gamma radiation / positive regulation of MAP kinase activity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / small GTPase binding / positive regulation of GTPase activity / 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 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 nucleoside triphosphate hydrolase
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: 1.6 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 5, 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)29,6604
Polymers29,1142
Non-polymers5472
Water5,621312
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)101.238, 101.238, 124.371
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 / HRAS / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 19403.904 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: 9710.006 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 / 5'-Guanylyl imidodiphosphate


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 / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3.16 Å3/Da / Density % sol: 62.91 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 20000, Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 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: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.6→30.12 Å / Num. obs: 50105 / % possible obs: 99.94 % / Redundancy: 19.5 % / CC1/2: 1 / Rmerge(I) obs: 0.05986 / Net I/σ(I): 28.52
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 0.8162 / Num. unique obs: 4914 / CC1/2: 0.944

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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: 1.6→30.12 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 4821 5.12 %
Rwork0.1815 89263 -
obs0.1825 50089 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.76 Å2 / Biso mean: 29.6144 Å2 / Biso min: 12.4 Å2
Refinement stepCycle: final / Resolution: 1.6→30.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 33 312 2288
Biso mean--18 39.22 -
Num. residues----244
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.6-1.620.26191590.25922976
1.62-1.640.23861470.25783010
1.64-1.660.31571650.2632952
1.66-1.680.3171480.23782967
1.68-1.70.2291380.24093015
1.7-1.720.20651650.21942968
1.72-1.750.23041940.21622961
1.75-1.770.241560.20932986
1.77-1.80.2311600.20262986
1.8-1.830.22941450.1982948
1.83-1.860.23171810.19462970
1.86-1.90.20711310.19622982
1.9-1.930.22211680.19362981
1.93-1.970.20581350.2033000
1.97-2.020.20651680.20022963
2.02-2.060.20891490.18943013
2.06-2.110.22961770.18382948
2.11-2.170.20941920.18722931
2.17-2.240.19912090.18162922
2.24-2.310.19781840.18042981
2.31-2.390.18581640.18252950
2.39-2.490.18831590.17962967
2.49-2.60.19611650.18382989
2.6-2.740.19471430.18693001
2.74-2.910.19881250.18723004
2.91-3.130.19161630.17692965
3.13-3.450.19211590.16672986
3.45-3.940.19611540.1512965
3.94-4.960.1521620.15162994
4.97-30.120.22141560.19012982
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)
11.85420.06580.36481.32630.15791.3030.18010.0285-0.05140.1575-0.1808-0.182-0.2650.279-0.0350.1497-0.093-0.02420.23320.05130.1873-21.556434.483524.4629
21.4821-0.05150.68021.2112-0.21550.99150.09480.03650.18030.2663-0.135-0.0436-0.24270.27730.00720.201-0.1353-0.01560.29940.03180.2026-22.936639.0928.5311
32.42590.0989-0.46392.0561-0.06772.9512-0.00770.14910.1563-0.1057-0.07430.2705-0.0105-0.24020.10540.1903-0.0668-0.02440.26310.03270.1986-26.555934.31917.8805
41.3260.6424-0.91661.8175-2.0282.5314-0.14480.2513-0.2623-0.31490.12830.1220.4808-0.2794-0.02750.1944-0.1041-0.03130.2189-0.01420.206-30.947723.52520.9452
51.72640.8992-0.9542.77760.22841.71280.06630.0206-0.24960.0662-0.0178-0.03830.3059-0.0804-0.03960.1634-0.0626-0.0440.20280.03550.2112-25.898321.450827.56
61.04180.3864-0.22122.0855-0.80081.860.1344-0.1252-0.12710.0853-0.2416-0.24540.16170.33490.05580.1408-0.0428-0.04530.24480.05240.2318-19.138722.01126.2447
75.0394-1.832-1.40552.6549-0.44173.12770.0927-0.00010.01380.1758-0.11640.1401-0.2192-0.09580.00490.1919-0.07710.00030.1950.01390.1822-31.050146.960420.251
85.44661.4830.91015.45762.51596.2263-0.1075-0.37650.12930.4439-0.15510.8574-0.5304-0.28820.06660.28530.02590.09210.37680.02930.3084-42.19454.399225.2928
92.9674-2.88840.45786.33820.20772.8298-0.2191-0.2370.0240.74220.12910.017-0.1307-0.01530.03360.3595-0.10840.03250.34650.01060.2091-29.441151.939629.0804
102.935-1.4257-0.99645.0996-2.82444.42540.1877-0.7159-0.030.9773-0.0573-0.253-0.04470.1304-0.16720.52-0.1515-0.07930.30180.02750.2502-23.481857.757126.6738
112.59931.110.41651.8949-0.03720.5143-0.0434-0.07250.5450.08160.14610.0332-0.2355-0.0299-0.05340.3496-0.0607-0.00550.1904-0.00680.252-29.96162.59519.6491
122.04110.2224-0.01481.85051.24768.1202-0.11570.02160.2363-0.1073-0.05990.5992-0.3477-0.85820.13970.28290.0030.0020.28750.00860.3-38.583758.031217.7024
133.77210.6794-1.68785.75171.07853.2199-0.0148-0.1531-0.11870.6263-0.0841-0.5217-0.046-0.06310.14280.3422-0.1003-0.07820.17730.04270.2181-24.776855.394620.7389
146.61053.16144.7963.62873.61624.3162-0.357-0.14190.07910.70190.0866-0.4269-0.08980.75580.24970.3533-0.0252-0.04070.3660.06630.3208-17.954759.859821.5617
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 46 )A26 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 74 )A47 - 74
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 104 )A75 - 104
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 126 )A105 - 126
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 166 )A127 - 166
7X-RAY DIFFRACTION7chain 'C' and (resid 277 through 293 )C277 - 293
8X-RAY DIFFRACTION8chain 'C' and (resid 294 through 300 )C294 - 300
9X-RAY DIFFRACTION9chain 'C' and (resid 301 through 313 )C301 - 313
10X-RAY DIFFRACTION10chain 'C' and (resid 314 through 327 )C314 - 327
11X-RAY DIFFRACTION11chain 'C' and (resid 328 through 340 )C328 - 340
12X-RAY DIFFRACTION12chain 'C' and (resid 341 through 347 )C341 - 347
13X-RAY DIFFRACTION13chain 'C' and (resid 348 through 353 )C348 - 353
14X-RAY DIFFRACTION14chain 'C' and (resid 354 through 358 )C354 - 358

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