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- PDB-9glw: NRas-Q61R-GTP in complex with the peptide MPB2 -

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Basic information

Entry
Database: PDB / ID: 9glw
TitleNRas-Q61R-GTP in complex with the peptide MPB2
Components
  • GTPase NRas
  • peptide MPB2
KeywordsHYDROLASE / GTPase / SIGNALING PROTEIN / SMALL G-PROTEIN
Function / homology
Function and homology information


Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS ...Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / positive regulation of endothelial cell proliferation / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / 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 / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / RAS processing / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / Signaling by BRAF and RAF1 fusions / DAP12 signaling / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / RAF/MAP kinase cascade / G protein activity / Ras protein signal transduction / Golgi membrane / GTPase activity / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / protein-containing complex binding / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTPase NRas
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOstermann, N. / Zink, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Identification and characterization of binders to a cryptic and functional pocket in KRAS.
Authors: Beyer, K.S. / Klein, J. / Katz, S. / Welker, P. / Lanter, M. / Guthy, D. / Pollehn, K. / Gluck-Gade, A. / Bleu, M. / Desogus, J. / Hattenberger, M. / Borrello, D. / Abdul Rahman, W. / Zink, ...Authors: Beyer, K.S. / Klein, J. / Katz, S. / Welker, P. / Lanter, M. / Guthy, D. / Pollehn, K. / Gluck-Gade, A. / Bleu, M. / Desogus, J. / Hattenberger, M. / Borrello, D. / Abdul Rahman, W. / Zink, F. / Ostermann, N. / Jahnke, W. / Dumelin, C.E. / Leder, L. / Esser, O. / Muller, L. / Marzinzik, A. / Cebe, R. / Muller, K. / Galli, G.G. / Tordella, L. / Cotesta, S. / Brachmann, S.M. / Maira, S.M.
History
DepositionAug 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase NRas
B: peptide MPB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9814
Polymers21,4332
Non-polymers5472
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.22, 112.22, 58.584
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

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Components

#1: Protein GTPase NRas / Transforming protein N-Ras


Mass: 19375.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01111, small monomeric GTPase
#2: Protein/peptide peptide MPB2


Mass: 2057.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cyclic peptide Li1 L1 / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 1000, 0.2 M Na2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.1→56.11 Å / Num. obs: 16013 / % possible obs: 99.7 % / Redundancy: 4.92 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.96
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.838 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 401 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RIZL

Resolution: 2.1→56.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.174 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.158
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 801 -RANDOM
Rwork0.1974 ---
obs0.1993 16013 99.7 %-
Displacement parametersBiso mean: 42.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.1169 Å20 Å20 Å2
2--1.1169 Å20 Å2
3----2.2338 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→56.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 179 123 1653
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081560HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.952115HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d543SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes268HARMONIC5
X-RAY DIFFRACTIONt_it1560HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion198SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1285SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion17.41
LS refinement shellResolution: 2.1→2.12 Å
RfactorNum. reflection% reflection
Rfree0.3799 20 -
Rwork0.3399 --
obs0.3422 401 98.99 %
Refinement TLS params.

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)
10.6511-0.02480.08041.0226-0.08230.5373-0.06370.0414-0.03030.0414-0.00090.031-0.03030.0310.0645-0.0225-0.02820.0387-0.0238-0.0353-0.006429.0365-19.39223.7301
20.6657-1.09740.32741.91340.49750.6847-0.08570.0302-0.23790.0302-0.07420.0351-0.23790.03510.15980.0431-0.0271-0.026-0.0305-0.0218-0.042325.8656-3.04738.3032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-1 - 168
2X-RAY DIFFRACTION1{ A|* }A202
3X-RAY DIFFRACTION2{ B|* }B1 - 16

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