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- PDB-9btm: NRas 1-169 Q61R in Complex with Shoc2 80-582 -

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Basic information

Entry
Database: PDB / ID: 9btm
TitleNRas 1-169 Q61R in Complex with Shoc2 80-582
Components
  • GTPase NRas
  • Leucine-rich repeat protein SHOC-2
KeywordsSIGNALING PROTEIN/HYDROLASE / SHOC2 / RAS / PP1C / MAPK / Complex / STRUCTURAL PROTEIN / SIGNALING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


cellular response to growth hormone stimulus / negative regulation of neural precursor cell proliferation / protein phosphatase type 1 complex / volume-sensitive anion channel activity / nerve growth factor signaling pathway / cyclic-GMP-AMP transmembrane import across plasma membrane / protein phosphatase 1 binding / protein phosphatase regulator activity / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling ...cellular response to growth hormone stimulus / negative regulation of neural precursor cell proliferation / protein phosphatase type 1 complex / volume-sensitive anion channel activity / nerve growth factor signaling pathway / cyclic-GMP-AMP transmembrane import across plasma membrane / protein phosphatase 1 binding / protein phosphatase regulator activity / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of Ras protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / regulation of MAPK cascade / 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 / fibroblast growth factor receptor signaling pathway / SHC1 events in ERBB4 signaling / negative regulation of neuron differentiation / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / 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 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / positive regulation of endothelial cell proliferation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / positive regulation of neuron differentiation / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / 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 / RAF activation / Signaling by ERBB2 TMD/JMD mutants / Signaling by high-kinase activity BRAF mutants / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of neuron projection development / RAS processing / Regulation of RAS by GAPs / Negative regulation of MAPK 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 / Signaling by BRAF and RAF1 fusions / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / MAPK cascade / DAP12 signaling / G protein activity / RAF/MAP kinase cascade / protein phosphatase binding / Ras protein signal transduction / intracellular signal transduction / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / Neutrophil degranulation / protein-containing complex binding / GTP binding / Golgi apparatus / extracellular exosome
Similarity search - Function
: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Leucine-rich repeat domain superfamily / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTPase NRas / Leucine-rich repeat protein SHOC-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsHauseman, Z.J. / King, D. / Viscomi, J. / Fodor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Nature / Year: 2025
Title: Targeting the SHOC2-RAS interaction in RAS-mutant cancers.
Authors: Hauseman, Z.J. / Stauffer, F. / Beyer, K.S. / Molle, S. / Cavicchioli, E. / Marchand, J.R. / Fodor, M. / Viscomi, J. / Dhembi, A. / Katz, S. / Faggion, B. / Lanter, M. / Kerr, G. / ...Authors: Hauseman, Z.J. / Stauffer, F. / Beyer, K.S. / Molle, S. / Cavicchioli, E. / Marchand, J.R. / Fodor, M. / Viscomi, J. / Dhembi, A. / Katz, S. / Faggion, B. / Lanter, M. / Kerr, G. / Schildknecht, D. / Handl, C. / Maddalo, D. / Pissot Soldermann, C. / Brady, J. / Shrestha, O. / Nguyen, Z. / Leder, L. / Cremosnik, G. / Lopez Romero, S. / Hassiepen, U. / Stams, T. / Linder, M. / Galli, G.G. / Guthy, D.A. / King, D.A. / Maira, S.M. / Thoma, C.R. / Ehmke, V. / Tordella, L.
History
DepositionMay 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Leucine-rich repeat protein SHOC-2
A: GTPase NRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3754
Polymers75,8272
Non-polymers5472
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.884, 89.339, 119.768
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Leucine-rich repeat protein SHOC-2 / Protein soc-2 homolog / Protein sur-8 homolog


Mass: 56583.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHOC2, KIAA0862 / Plasmid: pFastBac1 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UQ13
#2: Protein GTPase NRas / Transforming protein N-Ras


Mass: 19243.855 Da / Num. of mol.: 1 / Mutation: Q61R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRAS, HRAS1 / Plasmid: pET13b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01111, small monomeric GTPase
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Hepes pH 7, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→71.58 Å / Num. obs: 23050 / % possible obs: 100 % / Redundancy: 15 % / Biso Wilson estimate: 82.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Net I/σ(I): 13.2
Reflection shellResolution: 2.732→2.741 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 225 / CC1/2: 0.359 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→59.88 Å / SU ML: 0.4266 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6995
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1033 4.52 %RANDOM
Rwork0.2021 21796 --
obs0.2037 22829 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.23 Å2
Refinement stepCycle: LAST / Resolution: 2.73→59.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5205 0 33 9 5247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025320
X-RAY DIFFRACTIONf_angle_d0.49677211
X-RAY DIFFRACTIONf_chiral_restr0.0394861
X-RAY DIFFRACTIONf_plane_restr0.0033919
X-RAY DIFFRACTIONf_dihedral_angle_d14.68732052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.880.41021260.34082890X-RAY DIFFRACTION92.77
2.88-3.060.35691370.30853104X-RAY DIFFRACTION99.97
3.06-3.290.33521370.27923107X-RAY DIFFRACTION100
3.29-3.620.30371680.24913094X-RAY DIFFRACTION99.97
3.62-4.150.22931680.19323115X-RAY DIFFRACTION100
4.15-5.230.19231510.16773173X-RAY DIFFRACTION100
5.23-59.880.20191460.17463313X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: 15.0379552148 Å / Origin y: -7.13818575464 Å / Origin z: -11.0340941251 Å
111213212223313233
T0.571799528664 Å2-0.0261388752888 Å2-0.0384736700376 Å2-0.531626886097 Å20.0911677359146 Å2--0.47563653373 Å2
L1.76458554585 °2-0.488483458848 °20.55579660639 °2-1.13794148698 °2-0.162300491242 °2--0.806084251152 °2
S-0.179565048142 Å °0.0927641281009 Å °0.134504695253 Å °0.0968053347539 Å °0.156919056732 Å °0.0285614031328 Å °-0.0861195559415 Å °-0.114608845283 Å °0.0117763831208 Å °
Refinement TLS groupSelection details: all

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