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- PDB-9glx: NRas-Q61R-GTP in complex with the peptide MPB3 -

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Basic information

Entry
Database: PDB / ID: 9glx
TitleNRas-Q61R-GTP in complex with the peptide MPB3
Components
  • GTPase NRas
  • peptide MPB3
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: 1.85 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

Downloads & links

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Assembly

Deposited unit
A: GTPase NRas
B: GTPase NRas
C: GTPase NRas
D: GTPase NRas
E: GTPase NRas
F: GTPase NRas
G: peptide MPB3
K: peptide MPB3
N: peptide MPB3
Q: peptide MPB3
R: peptide MPB3
S: peptide MPB3
T: peptide MPB3
U: peptide MPB3
V: peptide MPB3
W: peptide MPB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,49028
Polymers134,20516
Non-polymers3,28512
Water20,3751131
1
A: GTPase NRas
G: peptide MPB3
Q: peptide MPB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5135
Polymers22,9663
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase NRas
R: peptide MPB3
S: peptide MPB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5135
Polymers22,9663
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTPase NRas
K: peptide MPB3
T: peptide MPB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5135
Polymers22,9663
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTPase NRas
N: peptide MPB3
U: peptide MPB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5135
Polymers22,9663
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: GTPase NRas
V: peptide MPB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7184
Polymers21,1712
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: GTPase NRas
W: peptide MPB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7184
Polymers21,1712
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.89, 121.26, 124.886
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19375.906 Da / Num. of mol.: 6
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 MPB3


Mass: 1795.002 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1131 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000, 0.2 M Lithium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.85→87 Å / Num. obs: 109131 / % possible obs: 100 % / Redundancy: 6.69 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 15.9
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 6.66 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 2183 / % possible all: 100

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Processing

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

Resolution: 1.85→69.64 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.144 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.127
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 5457 -RANDOM
Rwork0.1837 ---
obs0.1856 109131 100 %-
Displacement parametersBiso mean: 26.53 Å2
Baniso -1Baniso -2Baniso -3
1--8.2869 Å20 Å20 Å2
2--5.6188 Å20 Å2
3---2.6681 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.85→69.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8051 0 1306 1131 10488
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089602HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9813064HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3240SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1646HARMONIC5
X-RAY DIFFRACTIONt_it9602HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1233SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8781SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion16.59
LS refinement shellResolution: 1.85→1.86 Å
RfactorNum. reflection% reflection
Rfree0.2867 109 -
Rwork0.241 --
obs0.2433 2183 100 %
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)
10.03190.1082-0.10331.0114-0.34161.3223-0.0336-0.22230.1411-0.2223-0.00140.03120.14110.03120.0350.03550.0080.0236-0.0439-0.0128-0.0241-36.4151-63.4202-22.2852
20.5974-0.0439-0.55040.99220.49091.86710.00080.01030.04230.0103-0.0343-0.14760.0423-0.14760.0336-0.0501-0.0105-0.0244-0.0078-0.0072-0.0358-49.0839-68.57865.4642
30.38590.40050.43861.22670.53521.22540.08020.14480.11280.1448-0.0102-0.06170.1128-0.0617-0.070.0294-0.0052-0.0072-0.04510.0056-0.0436-4.6403-31.00614.5396
40.4898-0.3076-0.24191.2110.47451.18690.0314-0.0983-0.0429-0.09830.0017-0.0166-0.0429-0.0166-0.0332-0.0019-0.00090.0004-0.04220.0048-0.0341-5.2173-39.6296-15.1252
50.44430.0993-0.54981.8479-0.43851.3071-0.06010.07480.06510.07480.0601-0.02590.0651-0.0259-0-0.03320.0019-0.0053-0.032-0.0215-0.0256.0365-73.0563-21.9257
61.45940.1337-0.62641.19930.01811.6480.02970.1061-0.02340.10610.0041-0.0072-0.0234-0.0072-0.0337-0.03030.0035-0.0192-0.0385-0.0012-0.051-7.2658-78.65095.259
700.02440.01870.18250.01490.03020.0093-0.03-0.0248-0.03-0.0107-0.0278-0.0248-0.02780.00130.02570.0022-0.004-0.0176-0.0084-0.0382-19.4246-56.4495-5.7861
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 - 168
4X-RAY DIFFRACTION2{ B|* }B202
5X-RAY DIFFRACTION3{ C|* }C1 - 168
6X-RAY DIFFRACTION3{ C|* }C202
7X-RAY DIFFRACTION4{ D|* }D1 - 168
8X-RAY DIFFRACTION4{ D|* }D202
9X-RAY DIFFRACTION5{ E|* }E1 - 168
10X-RAY DIFFRACTION5{ E|* }E202
11X-RAY DIFFRACTION6{ F|* }F1 - 168
12X-RAY DIFFRACTION6{ F|* }F202
13X-RAY DIFFRACTION7{ Q|* }Q1 - 16

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