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- PDB-9c1b: Crystal structure of GDP-bound human M-RAS protein in crystal form II -

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Basic information

Entry
Database: PDB / ID: 9c1b
TitleCrystal structure of GDP-bound human M-RAS protein in crystal form II
ComponentsRas-related protein M-Ras
KeywordsHYDROLASE / M-RAS / GDP / GTPase structure / RAS / crystal packing
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
GUANOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Ras-related protein M-Ras
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsBester, S.M. / Abrahamsen, R. / Samora, L.R. / Wu, W.-I. / Mou, T.-C.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Crystal structure of the GDP-bound human M-RAS protein in two crystal forms.
Authors: Bester, S.M. / Abrahamsen, R. / Rodrigues Samora, L. / Wu, W.I. / Mou, T.C.
History
DepositionMay 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein M-Ras
B: Ras-related protein M-Ras
C: Ras-related protein M-Ras
D: Ras-related protein M-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,96517
Polymers101,3004
Non-polymers2,66513
Water6,323351
1
A: Ras-related protein M-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1375
Polymers25,3251
Non-polymers8124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein M-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9434
Polymers25,3251
Non-polymers6183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ras-related protein M-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0935
Polymers25,3251
Non-polymers7684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ras-related protein M-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7923
Polymers25,3251
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.724, 55.604, 67.770
Angle α, β, γ (deg.)103.737, 90.141, 93.636
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 25324.934 Da / Num. of mol.: 4
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

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Non-polymers , 6 types, 364 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.94 Å3/Da / Density % sol: 36.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→41.94 Å / Num. obs: 32348 / % possible obs: 91.29 % / Redundancy: 2.7 % / Biso Wilson estimate: 29.22 Å2 / CC1/2: 0.985 / Rpim(I) all: 0.049 / Rrim(I) all: 0.087 / Net I/σ(I): 11.81
Reflection shellResolution: 2.27→2.351 Å / Mean I/σ(I) obs: 3.71 / Num. unique obs: 3405 / CC1/2: 0.708 / Rpim(I) all: 0.207 / Rrim(I) all: 0.363

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→41.94 Å / SU ML: 0.2723 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.9418
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2469 1991 6.2 %
Rwork0.1992 30146 -
obs0.2021 32137 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.65 Å2
Refinement stepCycle: LAST / Resolution: 2.27→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 169 351 5932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025693
X-RAY DIFFRACTIONf_angle_d0.52727697
X-RAY DIFFRACTIONf_chiral_restr0.0428853
X-RAY DIFFRACTIONf_plane_restr0.0035963
X-RAY DIFFRACTIONf_dihedral_angle_d14.1791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.330.3241570.27242277X-RAY DIFFRACTION96.36
2.33-2.390.27971430.25162266X-RAY DIFFRACTION96.67
2.39-2.460.29671490.24212279X-RAY DIFFRACTION96.93
2.46-2.540.32641510.2542296X-RAY DIFFRACTION96.8
2.54-2.620.29031430.25012076X-RAY DIFFRACTION96.98
2.69-2.730.3168530.2509785X-RAY DIFFRACTION90.2
2.73-2.860.29791490.23682301X-RAY DIFFRACTION97.11
2.86-3.010.25161540.21732295X-RAY DIFFRACTION97.45
3.01-3.20.2751540.20542311X-RAY DIFFRACTION97.78
3.2-3.440.26451430.20022296X-RAY DIFFRACTION96.86
3.44-3.790.23271460.18032054X-RAY DIFFRACTION87.41
3.79-4.340.21081470.16152296X-RAY DIFFRACTION97.21
4.34-5.460.17811500.15752302X-RAY DIFFRACTION97.57
5.46-41.940.21981520.18842312X-RAY DIFFRACTION98.01

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