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- PDB-9mey: Crystal structure of RIT1(GDP) bound to LZTR1(Kelch domain) -

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Basic information

Entry
Database: PDB / ID: 9mey
TitleCrystal structure of RIT1(GDP) bound to LZTR1(Kelch domain)
Components
  • GTP-binding protein Rit1
  • Leucine-zipper-like transcriptional regulator 1
KeywordsONCOPROTEIN / Substrate adaptor
Function / homology
Function and homology information


Signalling to p38 via RIT and RIN / negative regulation of Ras protein signal transduction / Cul3-RING ubiquitin ligase complex / endomembrane system / small monomeric GTPase / small GTPase binding / recycling endosome membrane / GDP binding / G protein activity / Ras protein signal transduction ...Signalling to p38 via RIT and RIN / negative regulation of Ras protein signal transduction / Cul3-RING ubiquitin ligase complex / endomembrane system / small monomeric GTPase / small GTPase binding / recycling endosome membrane / GDP binding / G protein activity / Ras protein signal transduction / calmodulin binding / protein ubiquitination / GTPase activity / GTP binding / Golgi apparatus / signal transduction / plasma membrane
Similarity search - Function
: / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Kelch motif / Kelch / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain profile. ...: / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Kelch motif / Kelch / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / SKP1/BTB/POZ domain superfamily / 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 / Leucine-zipper-like transcriptional regulator 1 / GTP-binding protein Rit1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein Rit1
B: Leucine-zipper-like transcriptional regulator 1
C: GTP-binding protein Rit1
D: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,0488
Polymers118,1134
Non-polymers9354
Water1629
1
A: GTP-binding protein Rit1
B: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5244
Polymers59,0572
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-24 kcal/mol
Surface area21240 Å2
2
C: GTP-binding protein Rit1
D: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5244
Polymers59,0572
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-22 kcal/mol
Surface area20890 Å2
Unit cell
Length a, b, c (Å)148.582, 148.582, 130.728
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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.: 2
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: Protein Leucine-zipper-like transcriptional regulator 1 / LZTR-1


Mass: 36592.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LZTR1, TCFL2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N653
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.53 Å3/Da / Density % sol: 65.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 44% Morpheus II PPT7, 100mM MonoSach II, 100mM MB6 buffer pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2022
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.95→49.07 Å / Num. obs: 35502 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.035 / Rrim(I) all: 0.083 / Net I/σ(I): 18.4
Reflection shellResolution: 2.95→3.09 Å / Rmerge(I) obs: 1.471 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4675 / CC1/2: 0.796 / Rpim(I) all: 0.681

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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: 2.95→49.07 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2557 1775 5.01 %
Rwork0.2174 --
obs0.2193 35449 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7930 0 58 9 7997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028201
X-RAY DIFFRACTIONf_angle_d0.50511129
X-RAY DIFFRACTIONf_dihedral_angle_d14.912958
X-RAY DIFFRACTIONf_chiral_restr0.0411162
X-RAY DIFFRACTIONf_plane_restr0.0051451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.030.44011370.43052539X-RAY DIFFRACTION100
3.03-3.120.44141310.36992547X-RAY DIFFRACTION100
3.12-3.220.3581100.32182591X-RAY DIFFRACTION100
3.22-3.330.37381320.29942567X-RAY DIFFRACTION100
3.33-3.470.32151440.28682569X-RAY DIFFRACTION100
3.47-3.630.30131540.29612541X-RAY DIFFRACTION100
3.63-3.820.39761240.26162601X-RAY DIFFRACTION100
3.82-4.060.24331400.21672570X-RAY DIFFRACTION100
4.06-4.370.22421270.18942605X-RAY DIFFRACTION100
4.37-4.810.19141370.18482579X-RAY DIFFRACTION100
4.81-5.50.2061710.1892588X-RAY DIFFRACTION100
5.5-6.930.25051390.21352629X-RAY DIFFRACTION100
6.94-49.070.2331290.17392748X-RAY DIFFRACTION100
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)
14.30660.37020.05214.1839-0.91374.96670.23450.23730.00450.2006-0.02880.1781-0.35490.0143-0.1920.55080.17070.01930.79960.04250.6075-92.115967.735511.5248
23.49310.3010.54122.62360.6632.76210.10360.301-0.0989-0.07990.0557-0.03190.0152-0.3155-0.14310.46070.0425-0.02450.75870.02540.5895-68.116954.3549-8.5443
30.65820.7307-1.40773.16670.89217.7604-0.11580.9693-0.1017-0.21270.6798-0.20460.0930.6101-0.54710.7725-0.0375-0.25821.396-0.0671.0629-20.508144.4934-8.6912
43.33540.4012-1.45173.6660.91973.97680.01030.6375-0.46130.04090.3174-0.0191.2462-0.8171-0.331.2861-0.0782-0.47631.1457-0.04871.0013-37.277923.830212.0473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 19 through 193)
2X-RAY DIFFRACTION2(chain 'B' and resid 49 through 422)
3X-RAY DIFFRACTION3(chain 'C' and resid 19 through 193)
4X-RAY DIFFRACTION4(chain 'D' and resid 49 through 422)

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