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- PDB-9mf0: Crystal structure of KRAS(GDP) bound to LZTR1(Kelch domain) -

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Basic information

Entry
Database: PDB / ID: 9mf0
TitleCrystal structure of KRAS(GDP) bound to LZTR1(Kelch domain)
Components
  • Isoform 2B of GTPase KRas
  • Leucine-zipper-like transcriptional regulator 1
KeywordsONCOPROTEIN / Substrate adaptor
Function / homology
Function and homology information


negative regulation of Ras protein signal transduction / response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / Cul3-RING ubiquitin ligase complex / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity ...negative regulation of Ras protein signal transduction / response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / Cul3-RING ubiquitin ligase complex / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / myoblast proliferation / skeletal muscle cell differentiation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / cardiac muscle cell proliferation / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / protein-membrane adaptor activity / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / EGFR Transactivation by Gastrin / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / GRB2 events in ERBB2 signaling / homeostasis of number of cells within a tissue / CD209 (DC-SIGN) signaling / Downstream signal transduction / endomembrane system / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / response to glucocorticoid / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / liver development / Signaling by ERBB2 TMD/JMD mutants / RAF activation / female pregnancy / Signaling by high-kinase activity BRAF mutants / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / visual learning / Signaling by CSF1 (M-CSF) in myeloid cells / RAS processing / Regulation of RAS by GAPs / small GTPase binding / Negative regulation of MAPK pathway / cytoplasmic side of plasma membrane / recycling endosome membrane / cytokine-mediated signaling pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding
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 / GTPase KRas / Leucine-zipper-like transcriptional regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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: Isoform 2B of GTPase KRas
B: Leucine-zipper-like transcriptional regulator 1
C: Isoform 2B of GTPase KRas
D: Leucine-zipper-like transcriptional regulator 1
E: Isoform 2B of GTPase KRas
F: Leucine-zipper-like transcriptional regulator 1
G: Isoform 2B of GTPase KRas
H: Leucine-zipper-like transcriptional regulator 1
I: Isoform 2B of GTPase KRas
J: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,50220
Polymers279,16410
Non-polymers2,33810
Water46826
1
A: Isoform 2B of GTPase KRas
B: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3004
Polymers55,8332
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-20 kcal/mol
Surface area20370 Å2
2
C: Isoform 2B of GTPase KRas
D: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3004
Polymers55,8332
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-20 kcal/mol
Surface area20130 Å2
3
E: Isoform 2B of GTPase KRas
F: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3004
Polymers55,8332
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-18 kcal/mol
Surface area19990 Å2
4
G: Isoform 2B of GTPase KRas
H: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3004
Polymers55,8332
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-20 kcal/mol
Surface area20350 Å2
5
I: Isoform 2B of GTPase KRas
J: Leucine-zipper-like transcriptional regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3004
Polymers55,8332
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-23 kcal/mol
Surface area20330 Å2
Unit cell
Length a, b, c (Å)129.736, 138.300, 199.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Isoform 2B of GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19240.748 Da / Num. of mol.: 5 / Mutation: T35A, E62A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01116, 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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 8% w/v PGA-LM. 0.3M sodium malonate dibasic monohydrate, 0.1M sodium acetate pH 5.0.

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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: Dec 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 3.3→61.04 Å / Num. obs: 54824 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.332 / Rpim(I) all: 0.148 / Net I/σ(I): 6.6
Reflection shellResolution: 3.3→3.4 Å / Rmerge(I) obs: 1.647 / Num. unique obs: 4446 / CC1/2: 0.624 / Rpim(I) all: 0.72

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→59.21 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2334 2694 4.93 %
Rwork0.1861 --
obs0.1884 54694 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→59.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19471 0 145 26 19642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320130
X-RAY DIFFRACTIONf_angle_d0.58727302
X-RAY DIFFRACTIONf_dihedral_angle_d10.362747
X-RAY DIFFRACTIONf_chiral_restr0.0442867
X-RAY DIFFRACTIONf_plane_restr0.0063546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.360.37221390.3022684X-RAY DIFFRACTION99
3.36-3.420.33951330.28622699X-RAY DIFFRACTION100
3.42-3.490.35041420.27192689X-RAY DIFFRACTION100
3.49-3.570.33811480.26792704X-RAY DIFFRACTION100
3.57-3.650.30991410.25212700X-RAY DIFFRACTION100
3.65-3.740.27831310.23622701X-RAY DIFFRACTION100
3.74-3.840.29251180.22132737X-RAY DIFFRACTION100
3.84-3.960.23931490.20092699X-RAY DIFFRACTION100
3.96-4.090.23411420.1862716X-RAY DIFFRACTION100
4.09-4.230.21361570.1772698X-RAY DIFFRACTION100
4.23-4.40.18191490.15332707X-RAY DIFFRACTION100
4.4-4.60.18861440.14632742X-RAY DIFFRACTION100
4.6-4.840.1661250.13372745X-RAY DIFFRACTION100
4.84-5.150.16571500.13542740X-RAY DIFFRACTION100
5.15-5.540.20621450.1532757X-RAY DIFFRACTION100
5.54-6.10.26611430.16732750X-RAY DIFFRACTION100
6.1-6.980.21271280.16762802X-RAY DIFFRACTION100
6.98-8.790.19831380.16852817X-RAY DIFFRACTION100
8.8-59.210.21561720.17582913X-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)
12.76281.21180.59864.67130.08072.94750.0456-0.47210.03620.10520.1586-0.01630.0049-0.0594-0.18040.15240.00510.00180.5239-0.02660.42239.1692-43.1071-14.4064
24.2916-4.3043-1.8877.69180.28757.4269-0.3880.56310.2020.12530.0543-0.2173-0.4882-0.07420.30950.2945-0.1054-0.18910.4919-0.0050.693715.0963-52.5867-21.7783
33.32410.25281.011.87920.42122.689-0.2730.18520.2018-0.21630.059-0.079-0.15840.19040.2110.2289-0.0517-0.00980.4908-0.05470.539939.3527-28.8966-10.5415
45.32361.3196-0.87083.87610.66243.4491-0.0208-0.2436-0.06460.23210.15750.0167-0.1119-0.0327-0.11970.17830.0857-0.04770.35580.05350.386149.0929-18.231926.2353
55.78380.18551.68565.5647-0.77813.79580.16430.44240.38070.1824-0.54440.09160.0776-0.16020.35590.25870.0197-0.13990.5426-0.10270.666849.784-7.174218.73
61.9161-0.5384-0.92832.6533-0.12752.3966-0.05220.23810.07770.1150.0830.3403-0.0141-0.4088-0.03690.23010.09210.02370.55480.09550.471316.0952-12.643729.8112
74.68910.08730.21986.1093-0.96062.45380.4166-0.27870.4564-0.0402-0.02310.3061-0.48960.0482-0.37680.7409-0.14930.13640.4969-0.04060.323127.92510.1691-55.3359
83.34240.9352-1.05413.0121-1.26092.8817-0.11160.1719-0.212-0.55540.11330.18780.0502-0.08950.01140.454-0.1143-0.1110.39660.01770.478111.9754-29.0804-50.8295
92.8908-0.4617-0.02031.72210.07881.4836-0.0361-0.1075-0.14460.96620.36650.8085-0.22-0.4105-0.28090.93990.26760.40610.65860.16090.81071.3972-15.753565.9846
108.94694.36537.48996.46953.08717.29520.04830.0749-0.56160.0785-0.32040.24050.28490.23470.21730.6590.00330.24621.03280.49831.4033-5.8511-24.226558.3884
111.5530.82210.39372.5729-0.15042.4506-0.019-0.00880.07520.38580.01260.07910.1050.10930.01320.76210.22380.17890.45640.02150.395424.9539-39.817168.8757
123.19471.29010.0213.26-0.59543.20770.2784-0.1181-0.34970.3307-0.0803-0.51220.59990.5091-0.1791.44930.2632-0.02910.65180.02470.560639.0089-47.2369104.8449
133.34632.53841.50729.331-0.68494.0851-0.2710.051-0.21990.1097-0.15220.0172-0.0717-0.13940.39041.55440.473-0.03751.6139-0.4051.149.8373-44.568297.1226
142.44390.39870.29011.61720.53232.45660.19090.1690.3341-0.0275-0.080.0285-0.13750.0676-0.09741.29660.02730.26570.5550.06470.513934.7586-13.9822108.549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 169)
2X-RAY DIFFRACTION2(chain 'A' and resid 202 through 202)
3X-RAY DIFFRACTION3(chain 'B' and resid 49 through 422)
4X-RAY DIFFRACTION4(chain 'D' and resid 49 through 169)
5X-RAY DIFFRACTION5(chain 'D' and resid 202 through 202)
6X-RAY DIFFRACTION6(chain 'E' and resid 49 through 168)
7X-RAY DIFFRACTION7(chain 'G' and resid 1 through 202)
8X-RAY DIFFRACTION8(chain 'H' and resid 49 through 422)
9X-RAY DIFFRACTION9(chain 'J' and resid 49 through 169)
10X-RAY DIFFRACTION10(chain 'J' and resid 202 through 202)
11X-RAY DIFFRACTION11(chain 'F' and resid 49 through 422)
12X-RAY DIFFRACTION12(chain 'C' and resid 0 through 169)
13X-RAY DIFFRACTION13(chain 'C' and resid 202 through 202)
14X-RAY DIFFRACTION14(chain 'I' and resid 49 through 169)

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