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- PDB-9mf1: Crystal structure of RIT1 in the GDP state -

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Basic information

Entry
Database: PDB / ID: 9mf1
TitleCrystal structure of RIT1 in the GDP state
ComponentsGTP-binding protein Rit1
KeywordsONCOPROTEIN / Substrate adaptor
Function / homology
Function and homology information


Signalling to p38 via RIT and RIN / small monomeric GTPase / GDP binding / G protein activity / Ras protein signal transduction / calmodulin binding / GTPase activity / GTP binding / signal transduction / 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 / GTP-binding protein Rit1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDharmaiah, S. / Bonsor, D.A. / Simanshu, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)75N91019D00024 United States
CitationJournal: Science / Year: 2025
Title: Structural basis for LZTR1 recognition of RAS GTPases for degradation.
Authors: Dharmaiah, S. / Bonsor, D.A. / Mo, S.P. / Fernandez-Cabrera, A. / Chan, A.H. / Messing, S. / Drew, M. / Vega, M. / Nissley, D.V. / Esposito, D. / Castel, P. / Simanshu, D.K.
History
DepositionDec 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding protein Rit1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3007
Polymers22,4651
Non-polymers8366
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer by gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.577, 66.155, 124.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein GTP-binding protein Rit1 / Ras-like protein expressed in many tissues / Ras-like without CAAX protein 1


Mass: 22464.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIT1, RIBB, RIT, ROC1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q92963, small monomeric GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 10% w/v PEG 6000, 0.1M Bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.2→45.38 Å / Num. obs: 15121 / % possible obs: 97.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 28.85 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.088 / Net I/σ(I): 4.7
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.675 / Num. unique obs: 3561 / CC1/2: 0.727 / Rpim(I) all: 0.652 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.38 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 751 4.98 %
Rwork0.1797 --
obs0.1822 15087 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 53 158 1661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021533
X-RAY DIFFRACTIONf_angle_d0.5452062
X-RAY DIFFRACTIONf_dihedral_angle_d15.15224
X-RAY DIFFRACTIONf_chiral_restr0.041219
X-RAY DIFFRACTIONf_plane_restr0.004263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.370.31551310.26622872X-RAY DIFFRACTION98
2.37-2.610.29131620.23622797X-RAY DIFFRACTION97
2.61-2.990.26421510.20062915X-RAY DIFFRACTION99
2.99-3.760.22851360.16232902X-RAY DIFFRACTION97
3.76-45.380.18391710.14272850X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 6.4466 Å / Origin y: 25.1329 Å / Origin z: -23.4509 Å
111213212223313233
T0.1534 Å20.0018 Å2-0.0163 Å2-0.1807 Å2-0.0246 Å2--0.1967 Å2
L2.7338 °2-0.0177 °20.1093 °2-3.1855 °20.6899 °2--1.5912 °2
S-0.0229 Å °0.0292 Å °-0.0476 Å °0.0445 Å °0.0935 Å °-0.0762 Å °-0.009 Å °0.0517 Å °-0.0602 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 18 through 505)

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