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- PDB-9b4r: Crystal structure of MRAS bound to GMPPNP -

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Basic information

Entry
Database: PDB / ID: 9b4r
TitleCrystal structure of MRAS bound to GMPPNP
ComponentsRas-related protein M-Ras
KeywordsONCOPROTEIN / RAS / RRAS3 / MRAS
Function / homology
Function and homology information


protein phosphatase type 1 complex / GTP-dependent protein binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / cellular response to leukemia inhibitory factor / small monomeric GTPase / RAF activation / GDP binding / G protein activity / actin cytoskeleton organization ...protein phosphatase type 1 complex / GTP-dependent protein binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / cellular response to leukemia inhibitory factor / small monomeric GTPase / RAF activation / GDP binding / G protein activity / actin cytoskeleton organization / Ras protein signal transduction / GTPase activity / GTP binding / plasma membrane
Similarity search - Function
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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein M-Ras
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCzyzyk, D.J. / Simanshu, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)75N91019D00024 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into isoform-specific RAS-PI3K alpha interactions and the role of RAS in PI3K alpha activation.
Authors: Czyzyk, D. / Yan, W. / Messing, S. / Gillette, W. / Tsuji, T. / Yamaguchi, M. / Furuzono, S. / Turner, D.M. / Esposito, D. / Nissley, D.V. / McCormick, F. / Simanshu, D.K.
History
DepositionMar 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein M-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1455
Polymers19,4671
Non-polymers6774
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.481, 65.481, 107.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-374-

HOH

21A-434-

HOH

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Components

#1: Protein Ras-related protein M-Ras / Ras-related protein R-Ras3


Mass: 19467.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRAS, RRAS3 / Production host: Escherichia coli (E. coli) / References: UniProt: O14807, small monomeric GTPase
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.81 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.002 M divalent II mix, 50%v/v(30%w/v PEG 3000, 40%v/v 1,2,4-butanetriol, and 2%w/v NDSB 256)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.19556 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19556 Å / Relative weight: 1
ReflectionResolution: 2.1→42.54 Å / Num. obs: 14328 / % possible obs: 99.2 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.109 / Net I/σ(I): 15.17
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.1-2.220.74722140.7680.8061
2.22-2.380.51320980.9420.5461
2.38-2.570.34320040.9690.3661
2.57-2.810.22518490.9840.2391
2.81-3.140.13416800.9930.1431
3.14-3.620.07715120.9980.0821
3.62-4.430.05312900.9980.0561
4.43-6.240.04710340.9990.051
6.24-42.540.0386470.9990.0411

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.54 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 716 5 %
Rwork0.199 --
obs0.2015 14321 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→42.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 35 170 1521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031376
X-RAY DIFFRACTIONf_angle_d0.5331865
X-RAY DIFFRACTIONf_dihedral_angle_d11.072533
X-RAY DIFFRACTIONf_chiral_restr0.043207
X-RAY DIFFRACTIONf_plane_restr0.004234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.260.37131380.31112618X-RAY DIFFRACTION98
2.26-2.490.2751400.2322661X-RAY DIFFRACTION100
2.49-2.840.2481420.2212705X-RAY DIFFRACTION100
2.85-3.580.26181440.18232726X-RAY DIFFRACTION100
3.58-42.540.21571520.17472895X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.3125 Å / Origin y: -25.0908 Å / Origin z: 16.6752 Å
111213212223313233
T0.1853 Å20.0235 Å2-0.0072 Å2-0.2295 Å2-0.0003 Å2--0.2194 Å2
L3.9109 °21.3636 °21.0224 °2-2.1453 °20.6033 °2--2.7473 °2
S-0.0021 Å °-0.2315 Å °-0.0114 Å °0.0885 Å °-0.0116 Å °-0.1349 Å °0.0272 Å °0.1694 Å °0.0157 Å °
Refinement TLS groupSelection details: all

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