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- PDB-7vvb: Crystal Structure of KRas4A(GMPPNP-bound) in complex with the Ras... -

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Basic information

Entry
Database: PDB / ID: 7vvb
TitleCrystal Structure of KRas4A(GMPPNP-bound) in complex with the Ras-binding domain(RBD) of SIN1
Components
  • GTPase KRas
  • 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 / serine/threonine protein kinase complex / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / response to mineralocorticoid / GMP binding ...TORC2 signaling / TORC2 complex / regulation of cellular response to oxidative stress / phosphatidic acid binding / negative regulation of Ras protein signal transduction / serine/threonine protein kinase complex / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / Constitutive Signaling by AKT1 E17K in Cancer / type I pneumocyte differentiation / Rac protein signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / myoblast proliferation / skeletal muscle cell differentiation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / CD28 dependent PI3K/Akt signaling / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / enzyme-substrate adaptor activity / cardiac muscle cell proliferation / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / 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 CSF3 (G-CSF) / 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 / striated muscle cell differentiation / Signaling by FGFR2 in disease / phosphatidylinositol-4,5-bisphosphate binding / cytoskeleton organization / 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 / homeostasis of number of cells within a tissue / 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 / response to glucocorticoid / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / VEGFR2 mediated vascular permeability / FCERI mediated MAPK activation / liver development / female pregnancy / RAF activation / Signaling by ERBB2 TMD/JMD mutants / 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
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. / Ran (Ras-related nuclear proteins) /TC4 subfamily of 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. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 KRas / 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 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
B: Target of rapamycin complex 2 subunit MAPKAP1
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4974
Polymers80,9512
Non-polymers5472
Water4,630257
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)101.660, 101.660, 124.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

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Components

#1: 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: 59206.738 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
#2: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 21743.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116, small monomeric GTPase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 1.15 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG 5000 MME

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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: Jan 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→22.38 Å / Num. obs: 79142 / % possible obs: 99.78 % / Redundancy: 18.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0682 / Net I/σ(I): 26.68
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 15.8 % / Rmerge(I) obs: 0.5955 / Num. unique obs: 4143 / CC1/2: 0.949 / % possible all: 99.98

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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→22.38 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 3811 4.82 %
Rwork0.1727 75331 -
obs0.1739 79142 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.99 Å2 / Biso mean: 33.0566 Å2 / Biso min: 12.11 Å2
Refinement stepCycle: final / Resolution: 1.7→22.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 33 257 2244
Biso mean--22.48 43.02 -
Num. residues----244
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.720.29361340.25622823100
1.72-1.740.25941540.24772797100
1.74-1.770.24241610.21592743100
1.77-1.790.24281350.21822812100
1.79-1.820.191180.20782819100
1.82-1.850.24291330.19522821100
1.85-1.880.23761480.19982764100
1.88-1.910.2681510.19542774100
1.91-1.950.24871670.19582742100
1.95-1.980.21161710.19392783100
1.98-2.020.24881310.19682786100
2.02-2.070.21041370.18562809100
2.07-2.120.20891280.17882812100
2.12-2.170.20271650.18282764100
2.17-2.230.19111410.17862796100
2.23-2.290.22191310.16822802100
2.29-2.370.22031470.16892771100
2.37-2.450.19861510.17892778100
2.45-2.550.20921600.18082781100
2.55-2.670.17531300.182818100
2.67-2.810.2361400.18562784100
2.81-2.980.16751060.18562828100
2.98-3.210.19591470.15882780100
3.21-3.530.16071310.15972792100
3.53-4.040.17831320.1463278599
4.05-5.090.16531330.14272801100
5.09-22.380.20071290.1838276699
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)
14.444-3.60130.77072.99680.09892.8379-0.01170.55910.7454-0.1783-0.0862-0.5062-0.38530.03230.10710.1779-0.01790.01070.20870.07420.2632-26.464354.2417-1.4094
25.5509-4.95070.08749.13920.76644.00590.44360.92810.1944-0.8293-0.595-0.2722-0.20260.05880.15610.32730.00410.01710.48250.06740.2424-30.729451.4824-8.5206
35.35942.68711.47363.00072.14092.5019-0.4436-0.2378-0.3413-0.4130.20930.3056-0.4123-0.38160.56940.73790.2189-0.19111.047-0.18640.4278-36.907245.5277-13.822
45.6686-1.0096-1.17074.10281.8532.25220.33590.1984-0.25250.5077-0.12010.31040.055-0.4845-0.10520.17230.0371-0.02110.39990.00220.2621-38.9951.4801-1.4741
54.37510.57080.79632.8985-0.85694.129-0.04740.13710.3323-0.11440.15550.4333-0.3256-0.5158-0.05940.24690.0507-0.01820.32440.0110.2844-39.828257.2580.8079
66.9901-4.06441.33195.91750.17455.7581-0.713-0.3981.17620.77160.2911-0.3555-1.4999-0.09920.42940.37870.0226-0.08940.2272-0.00110.2988-31.683462.4922.8793
78.6125-1.73370.88553.5915-3.01267.29250.048-0.013-0.83250.2520.02680.11090.335-0.49810.08950.17720.01530.00870.3051-0.02210.266-36.063949.114-0.0239
86.41090.42944.7731.6117-0.42686.51720.19920.62570.2867-0.6855-0.02590.96070.3364-0.6805-0.22970.5067-0.0495-0.01110.5708-0.0380.5634-43.121345.3258-0.886
91.76040.0275-0.16932.7913-0.65822.7834-0.07770.4459-0.18250.10770.15360.08790.0744-0.4887-0.07570.1328-0.03640.01640.2637-0.02340.1854-19.765235.7318-3.4812
103.29660.58070.50945.46423.3594.9371-0.00761.08260.4538-0.4307-0.35850.6415-0.32-0.49960.19660.21630.00750.02270.54940.07560.3625-19.448744.3557-12.9474
112.2052.1179-0.19547.1687-0.51.852-0.00980.0497-0.03360.0087-0.001-0.02860.1096-0.0656-0.0130.1887-0.03790.01440.26590.00180.1941-23.452834.1131-0.908
123.7470.33730.92218.5805-3.83135.8276-0.2220.23980.77840.35230.1326-0.2492-0.7946-0.17090.23470.3921-0.0488-0.0350.4113-0.05240.3822-12.580346.43375.9475
133.3471.3889-4.00051.4412-1.20926.28550.0281-0.02070.04480.07770.0096-0.11820.01760.0208-0.0470.1511-0.012-0.00110.29160.00910.2341-8.866536.2184-4.4289
142.81030.1314-3.41440.6665-0.77534.34880.2261-0.7694-0.03960.3685-0.1937-0.4315-0.64691.61050.00580.2322-0.0758-0.05460.4124-0.02910.3222-2.476339.92171.8506
152.0156-0.5627-1.21611.88810.8526.9905-0.094-0.1843-0.22390.21940.0847-0.2820.54720.8640.1090.1940.0011-0.02110.29320.01050.2906-7.91931.89174.4656
163.45010.38731.14060.11480.46651.7708-0.00761.4701-0.3782-0.3462-0.1342-0.22490.4263-0.17350.19110.2558-0.03770.08130.5738-0.06070.3584-3.766335.0654-17.6657
174.55220.6538-2.35733.090.43892.085-0.2831-0.4141-0.76170.05290.314-0.14910.73120.64910.02570.23280.04620.0120.35630.02440.351.993628.6208-4.5574
186.7916-2.38993.03273.8646-2.40486.64960.19210.9897-0.8966-0.3691-0.09620.30590.60670.1858-0.02820.2209-0.06330.05290.38-0.0730.3004-11.300429.3534-11.2138
194.09931.46920.01933.756-0.57978.1252-0.307-0.0264-0.7408-0.11220.048-0.79681.11890.30920.24580.2787-0.04750.06750.2707-0.02030.4009-16.621125.0762-0.1618
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 278 through 300 )B278 - 300
2X-RAY DIFFRACTION2chain 'B' and (resid 301 through 313 )B301 - 313
3X-RAY DIFFRACTION3chain 'B' and (resid 314 through 322 )B314 - 322
4X-RAY DIFFRACTION4chain 'B' and (resid 323 through 327 )B323 - 327
5X-RAY DIFFRACTION5chain 'B' and (resid 328 through 340 )B328 - 340
6X-RAY DIFFRACTION6chain 'B' and (resid 341 through 347 )B341 - 347
7X-RAY DIFFRACTION7chain 'B' and (resid 348 through 353 )B348 - 353
8X-RAY DIFFRACTION8chain 'B' and (resid 354 through 358 )B354 - 358
9X-RAY DIFFRACTION9chain 'A' and (resid 0 through 25 )A0 - 25
10X-RAY DIFFRACTION10chain 'A' and (resid 26 through 36 )A26 - 36
11X-RAY DIFFRACTION11chain 'A' and (resid 37 through 61 )A37 - 61
12X-RAY DIFFRACTION12chain 'A' and (resid 62 through 74 )A62 - 74
13X-RAY DIFFRACTION13chain 'A' and (resid 75 through 86 )A75 - 86
14X-RAY DIFFRACTION14chain 'A' and (resid 87 through 103 )A87 - 103
15X-RAY DIFFRACTION15chain 'A' and (resid 104 through 116 )A104 - 116
16X-RAY DIFFRACTION16chain 'A' and (resid 117 through 126 )A117 - 126
17X-RAY DIFFRACTION17chain 'A' and (resid 127 through 137 )A127 - 137
18X-RAY DIFFRACTION18chain 'A' and (resid 138 through 151 )A138 - 151
19X-RAY DIFFRACTION19chain 'A' and (resid 152 through 166 )A152 - 166

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