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- PDB-7xkj: Kras-G12D-GDP-MRTX1133 by FIB-MicroED -

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Basic information

Entry
Database: PDB / ID: 7xkj
TitleKras-G12D-GDP-MRTX1133 by FIB-MicroED
ComponentsKRAS proto-oncogene, GTPase
KeywordsONCOPROTEIN / g12d / gdp / gtpase / hydrolase-hydrolase inhibitor complex / hydrolase/hydrolase inhibitor / MicroED
Function / homology
Function and homology information


small monomeric GTPase / GDP binding / Ras protein signal transduction / GTPase activity / GTP binding / plasma membrane
Similarity search - Function
Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain profile. / 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 ...Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain profile. / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6IC / GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3 Å
AuthorsLi, X.M.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: Kras-G12D-GDP-MRTX1133 by FIB-MicroED
Authors: Li, X.M.
History
DepositionApr 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / struct
Item: _citation.title / _struct.title
Revision 1.2Sep 17, 2025Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Structure summary
Category: em_3d_fitting_list / pdbx_entry_details ...em_3d_fitting_list / pdbx_entry_details / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KRAS proto-oncogene, GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3824
Polymers19,3141
Non-polymers1,0683
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-5 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.880, 49.280, 87.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein KRAS proto-oncogene, GTPase


Mass: 19313.730 Da / Num. of mol.: 1 / Mutation: G12D, C118S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: mMyoMyo1_007468 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J7Z4L6
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-6IC / 4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)-5-ethynyl-6-fluoronaphthalen-2-ol / MRTX-1133


Mass: 600.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H31F3N6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Isoform 2B of GTPase KRas GUANOSINE-5'-DIPHOSPHATE 4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d] ...Name: Isoform 2B of GTPase KRas GUANOSINE-5'-DIPHOSPHATE 4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)-5-ethynyl-6-fluoronaphthalen-2-ol MAGNESIUM ION
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.02 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

MicroscopyModel: JEOL 2100F
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal magnification: 6000 X / Calibrated magnification: 6000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 2300 nm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FISCHIONE 2550 / Temperature (max): 100 K / Temperature (min): 90 K
Image recordingAverage exposure time: 2 sec. / Electron dose: 0.02 e/Å2 / Detector mode: OTHER / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)
EM imaging opticsPhase plate: OTHER
EM diffractionCamera length: 100 mm
EM diffraction shellResolution: 3→33.17 Å / Fourier space coverage: 100 % / Multiplicity: 8.3 / Num. of structure factors: 3591 / Phase residual: 13.5 °
EM diffraction statsFourier space coverage: 100 % / High resolution: 3 Å / Num. of intensities measured: 29866 / Num. of structure factors: 3591 / Phase error rejection criteria: no / Rmerge: 0.4827
Diffraction sourceWavelength: 0.025
Radiation wavelengthWavelength: 0.025 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 44.23 Å2

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement / Contact author: Paul D. Adams / Contact author email: pdadams[at]lbl.gov / Language: Python/C++ / URL: https://www.phenix-online.org/ / Type: program
EM software
IDNameVersionCategoryDetails
6Coot0.9.4model fittingno
8PHENIX1.19.2model refinementno
9PHENIX1.19.2molecular replacement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 39.868 Å / B: 51.757 Å / C: 89.611 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionMethod: CRYSTALLOGRAPHY / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 200 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient / Details: no
Atomic model buildingPDB-ID: 7RPZ

7rpz


Pdb chain-ID: A / Accession code: 7RPZ / Pdb chain residue range: 1-169 / Source name: PDB / Type: experimental model
RefinementResolution: 3→35.51 Å / SU ML: 0.3835 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3366 651 10.15 %
Rwork0.31 5760 -
obs0.3134 6411 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.68 Å2
Refinement stepCycle: LAST / Resolution: 3→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 73 6 1406
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.01081433
ELECTRON CRYSTALLOGRAPHYf_angle_d1.64331952
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0915213
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0079243
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d17.3004529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.230.37571250.3241139ELECTRON CRYSTALLOGRAPHY98.37
3.23-3.560.32691310.32561164ELECTRON CRYSTALLOGRAPHY99.62
3.56-4.070.36571330.29651144ELECTRON CRYSTALLOGRAPHY99.61
4.07-5.120.30931320.27841159ELECTRON CRYSTALLOGRAPHY99.54
5.13-35.510.33141300.34391154ELECTRON CRYSTALLOGRAPHY98.92

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