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- PDB-9mez: Crystal structure of MRAS(GDP) bound to LZTR1(Kelch domain) -

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Basic information

Entry
Database: PDB / ID: 9mez
TitleCrystal structure of MRAS(GDP) bound to LZTR1(Kelch domain)
Components
  • Leucine-zipper-like transcriptional regulator 1
  • Ras-related protein M-Ras
KeywordsONCOPROTEIN / Substrate adaptor
Function / homology
Function and homology information


protein phosphatase type 1 complex / GTP-dependent protein binding / negative regulation of Ras protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Cul3-RING ubiquitin ligase complex / endomembrane system / cellular response to leukemia inhibitory factor / small monomeric GTPase / RAF activation ...protein phosphatase type 1 complex / GTP-dependent protein binding / negative regulation of Ras protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Cul3-RING ubiquitin ligase complex / endomembrane system / cellular response to leukemia inhibitory factor / small monomeric GTPase / RAF activation / small GTPase binding / recycling endosome membrane / GDP binding / G protein activity / actin cytoskeleton organization / Ras protein signal transduction / protein ubiquitination / GTPase activity / GTP binding / Golgi apparatus / 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
ACETATE ION / FORMIC ACID / GUANOSINE-5'-DIPHOSPHATE / MALONIC ACID / Ras-related protein M-Ras / Leucine-zipper-like transcriptional regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Ras-related protein M-Ras
B: Leucine-zipper-like transcriptional regulator 1
C: Ras-related protein M-Ras
D: Leucine-zipper-like transcriptional regulator 1
E: Ras-related protein M-Ras
F: Leucine-zipper-like transcriptional regulator 1
G: Ras-related protein M-Ras
H: Leucine-zipper-like transcriptional regulator 1
I: Ras-related protein M-Ras
J: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,61925
Polymers286,86410
Non-polymers2,75515
Water25214
1
A: Ras-related protein M-Ras
B: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8865
Polymers57,3732
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-21 kcal/mol
Surface area20430 Å2
2
C: Ras-related protein M-Ras
D: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9445
Polymers57,3732
Non-polymers5723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-24 kcal/mol
Surface area20380 Å2
3
E: Ras-related protein M-Ras
F: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9445
Polymers57,3732
Non-polymers5723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-23 kcal/mol
Surface area20390 Å2
4
G: Ras-related protein M-Ras
H: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0036
Polymers57,3732
Non-polymers6314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-24 kcal/mol
Surface area20620 Å2
5
I: Ras-related protein M-Ras
J: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8404
Polymers57,3732
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-23 kcal/mol
Surface area19570 Å2
Unit cell
Length a, b, c (Å)70.764, 110.788, 223.253
Angle α, β, γ (deg.)90.00, 94.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 10 molecules ACEGIBDFHJ

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


Mass: 20780.688 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRAS, RRAS3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O14807, small monomeric GTPase
#2: Protein
Leucine-zipper-like transcriptional regulator 1 / LZTR-1


Mass: 36592.066 Da / Num. of mol.: 5
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

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Non-polymers , 6 types, 29 molecules

#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 5 / 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.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 11.2% w/v PEG3350, 5.26% Tacsimate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2.8→49.22 Å / Num. obs: 84708 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.061 / Net I/σ(I): 9.7
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 1.554 / Mean I/σ(I) obs: 1 / Num. unique obs: 4499 / CC1/2: 0.578 / Rpim(I) all: 0.958

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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: 2.8→49.22 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 4125 4.88 %
Rwork0.2144 --
obs0.2164 84605 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19290 0 173 14 19477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00220000
X-RAY DIFFRACTIONf_angle_d0.60627216
X-RAY DIFFRACTIONf_dihedral_angle_d14.8017080
X-RAY DIFFRACTIONf_chiral_restr0.0462903
X-RAY DIFFRACTIONf_plane_restr0.0043521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.45821210.44082825X-RAY DIFFRACTION100
2.83-2.870.3991170.38872768X-RAY DIFFRACTION100
2.87-2.90.40311320.36112749X-RAY DIFFRACTION100
2.9-2.940.40991470.342790X-RAY DIFFRACTION100
2.94-2.980.3341370.32212774X-RAY DIFFRACTION100
2.98-3.020.37791450.32372711X-RAY DIFFRACTION100
3.02-3.070.39331250.30442845X-RAY DIFFRACTION100
3.07-3.120.34511480.28472710X-RAY DIFFRACTION100
3.12-3.170.29681300.27882781X-RAY DIFFRACTION100
3.17-3.220.31521390.27672807X-RAY DIFFRACTION100
3.22-3.280.34221290.28092760X-RAY DIFFRACTION100
3.28-3.350.31021370.2792788X-RAY DIFFRACTION100
3.35-3.410.31571390.27972739X-RAY DIFFRACTION100
3.41-3.490.34351580.28012753X-RAY DIFFRACTION100
3.49-3.570.39941440.28252832X-RAY DIFFRACTION100
3.57-3.660.34051390.28532713X-RAY DIFFRACTION100
3.66-3.760.32751500.27932770X-RAY DIFFRACTION99
3.76-3.870.25791520.21782743X-RAY DIFFRACTION100
3.87-3.990.2321300.20572825X-RAY DIFFRACTION100
3.99-4.140.23111250.1972777X-RAY DIFFRACTION100
4.14-4.30.23551750.18122714X-RAY DIFFRACTION99
4.3-4.50.17931560.1682716X-RAY DIFFRACTION98
4.5-4.730.1831700.15632762X-RAY DIFFRACTION99
4.73-5.030.19521530.16292774X-RAY DIFFRACTION100
5.03-5.420.22631290.16632818X-RAY DIFFRACTION100
5.42-5.960.22521350.1872806X-RAY DIFFRACTION100
5.96-6.820.27361570.19972765X-RAY DIFFRACTION100
6.82-8.590.22641570.18942811X-RAY DIFFRACTION100
8.59-49.220.21191490.18032854X-RAY DIFFRACTION99
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)
11.73230.68180.57822.3768-1.16072.9735-0.1617-0.13510.07920.10970.0795-0.70090.01810.63150.09270.40310.2372-0.06320.9813-0.1321.1005-1.758-5.0548.238
22.34070.6238-1.20652.74270.19382.9244-0.07150.1930.12680.11160.18720.1031-0.1283-0.1423-0.10250.45410.3215-0.06850.7567-0.01210.6766-33.8742.65954.128
32.56140.09910.39831.10090.16151.8431-0.1868-0.12940.11190.64410.40240.2208-0.3193-0.2557-0.21651.3130.57870.31360.89640.12780.8345-48.2693.23992.079
43.6563-0.0731-0.93832.44741.1283.69560.2551-0.3788-0.58290.5918-0.0718-0.04711.23520.0464-0.17491.1894-0.1589-0.14390.58020.1050.7048-15.218-27.547137.803
52.9558-0.61820.49242.3725-0.15884.11650.2651-0.33380.26720.4805-0.1351-0.02120.1947-0.2431-0.14350.7668-0.26570.0620.4903-0.0160.7131-28.1516.287182.787
61.77750.8982-1.57191.7472-0.69142.32050.2266-0.3645-0.29450.7586-0.66080.44132.0877-1.68320.42652.1112-0.96490.21862.10250.09151.0961-55.915-25.874221.153
72.26160.39840.87581.67150.03864.24550.12680.0948-0.15340.0509-0.01620.09-0.4946-0.2343-0.10020.64330.20020.12930.47230.05270.633-25.588-20.04899.638
82.638-0.6318-0.52792.24032.07436.36420.19810.09030.1349-0.2334-0.0032-0.2892-0.3238-0.368-0.14690.5491-0.15850.07920.50570.07020.6825-19.6225.012144.28
92.32710.42521.2632.72530.27532.47510.5369-0.6418-0.34181.1503-0.40870.16940.8615-0.5822-0.12291.3853-0.56020.09080.87650.08390.9591-45.287-12.423184.098
101.98340.07441.73831.9070.42797.5160.2335-0.0122-0.1544-0.38120.11920.00511.9129-0.3714-0.31491.2036-0.10850.13980.87410.1710.7661-27.309-12.72232.168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 10:179 OR RESID 201:201 ) )A10 - 179
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 10:179 OR RESID 201:201 ) )A201
3X-RAY DIFFRACTION2( CHAIN B AND RESID 49:330 )B49 - 330
4X-RAY DIFFRACTION3( CHAIN C AND ( RESID 10:179 OR RESID 201:201 ) )C10 - 179
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 10:179 OR RESID 201:201 ) )C201
6X-RAY DIFFRACTION4( CHAIN E AND ( RESID 11:179 OR RESID 201:201 ) )E11 - 179
7X-RAY DIFFRACTION4( CHAIN E AND ( RESID 11:179 OR RESID 201:201 ) )E201
8X-RAY DIFFRACTION5( CHAIN G AND ( RESID 11:180 OR RESID 201:201 ) )G11 - 180
9X-RAY DIFFRACTION5( CHAIN G AND ( RESID 11:180 OR RESID 201:201 ) )G201
10X-RAY DIFFRACTION6( CHAIN I AND ( RESID 11:177 OR RESID 201:201 ) )I11 - 177
11X-RAY DIFFRACTION6( CHAIN I AND ( RESID 11:177 OR RESID 201:201 ) )I201
12X-RAY DIFFRACTION7( CHAIN D AND RESID 49:330 )D49 - 330
13X-RAY DIFFRACTION8( CHAIN F AND RESID 49:330 )F49 - 330
14X-RAY DIFFRACTION9( CHAIN H AND RESID 49:330 )H49 - 330
15X-RAY DIFFRACTION10( CHAIN J AND RESID 49:330 )J49 - 330

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