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- PDB-7txh: Human MRas Q71R in complex with human Shoc2 LRR domain M173I and ... -

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Basic information

Entry
Database: PDB / ID: 7txh
TitleHuman MRas Q71R in complex with human Shoc2 LRR domain M173I and human PP1Ca
Components
  • Leucine-rich repeat protein SHOC-2
  • Ras-related protein M-Ras
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / RAS / PP1 / SHOC2 / LRR
Function / homology
Function and homology information


cellular response to growth hormone stimulus / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / negative regulation of neural precursor cell proliferation / protein phosphatase type 1 complex / volume-sensitive anion channel activity / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity ...cellular response to growth hormone stimulus / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / negative regulation of neural precursor cell proliferation / protein phosphatase type 1 complex / volume-sensitive anion channel activity / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / nerve growth factor signaling pathway / cyclic-GMP-AMP transmembrane import across plasma membrane / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / protein phosphatase regulator activity / GTP-dependent protein binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / dephosphorylation / positive regulation of Ras protein signal transduction / regulation of canonical Wnt signaling pathway / glycogen metabolic process / negative regulation of neuron differentiation / protein-serine/threonine phosphatase / branching morphogenesis of an epithelial tube / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / protein serine/threonine phosphatase activity / phosphatase activity / telomere maintenance in response to DNA damage / regulation of MAPK cascade / phosphoprotein phosphatase activity / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / DARPP-32 events / fibroblast growth factor receptor signaling pathway / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / positive regulation of neuron differentiation / lung development / cellular response to leukemia inhibitory factor / Downregulation of TGF-beta receptor signaling / small monomeric GTPase / adherens junction / circadian regulation of gene expression / positive regulation of transcription elongation by RNA polymerase II / RAF activation / positive regulation of neuron projection development / regulation of circadian rhythm / response to lead ion / GDP binding / : / presynapse / G protein activity / actin cytoskeleton organization / protein phosphatase binding / perikaryon / dendritic spine / Ras protein signal transduction / intracellular signal transduction / protein stabilization / iron ion binding / cell division / GTPase activity / GTP binding / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / : / Leucine-rich repeat region / Metallo-dependent phosphatases ...Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / : / Leucine-rich repeat region / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 / 4-Layer Sandwich / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / PHOSPHATE ION / Ras-related protein M-Ras / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Leucine-rich repeat protein SHOC-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHauseman, Z.J. / Viscomi, J. / Dhembi, A. / Clark, K. / King, D.A. / Fodor, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: Structure of the MRAS-SHOC2-PP1C phosphatase complex.
Authors: Hauseman, Z.J. / Fodor, M. / Dhembi, A. / Viscomi, J. / Egli, D. / Bleu, M. / Katz, S. / Park, E. / Jang, D.M. / Porter, K.A. / Meili, F. / Guo, H. / Kerr, G. / Molle, S. / Velez-Vega, C. / ...Authors: Hauseman, Z.J. / Fodor, M. / Dhembi, A. / Viscomi, J. / Egli, D. / Bleu, M. / Katz, S. / Park, E. / Jang, D.M. / Porter, K.A. / Meili, F. / Guo, H. / Kerr, G. / Molle, S. / Velez-Vega, C. / Beyer, K.S. / Galli, G.G. / Maira, S.M. / Stams, T. / Clark, K. / Eck, M.J. / Tordella, L. / Thoma, C.R. / King, D.A.
History
DepositionFeb 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 21, 2022Group: 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
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein M-Ras
B: Leucine-rich repeat protein SHOC-2
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Ras-related protein M-Ras
E: Leucine-rich repeat protein SHOC-2
F: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,66834
Polymers222,5026
Non-polymers3,16628
Water30,8961715
1
A: Ras-related protein M-Ras
B: Leucine-rich repeat protein SHOC-2
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,65015
Polymers111,2513
Non-polymers1,39912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ras-related protein M-Ras
E: Leucine-rich repeat protein SHOC-2
F: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,01819
Polymers111,2513
Non-polymers1,76716
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.959, 115.755, 137.804
Angle α, β, γ (deg.)90.000, 100.314, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Ras-related protein M-Ras / Ras-related protein R-Ras3


Mass: 20567.482 Da / Num. of mol.: 2 / Mutation: Q71R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRAS, RRAS3 / Production host: Escherichia coli (E. coli) / References: UniProt: O14807, small monomeric GTPase
#2: Protein Leucine-rich repeat protein SHOC-2 / Protein soc-2 homolog / Protein sur-8 homolog


Mass: 56719.543 Da / Num. of mol.: 2 / Mutation: M173I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHOC2, KIAA0862 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UQ13
#3: Protein Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 33963.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, protein-serine/threonine phosphatase

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Non-polymers , 6 types, 1743 molecules

#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#8: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1715 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M NaH2PO4 pH 6.5, 12% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→88.033 Å / Num. obs: 163294 / % possible obs: 99.86 % / Redundancy: 2 % / Biso Wilson estimate: 31.52 Å2 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.088 / Net I/σ(I): 10.49
Reflection shellResolution: 1.951→1.958 Å / Redundancy: 4.4 % / Num. unique obs: 1654 / CC1/2: 0.804 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
PHENIX1.19.2_4158refinement
PHASERphasing
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZK6, 1X1S

6zk6

1x1s


Resolution: 1.95→42.26 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.5049
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2103 8191 5.02 %
Rwork0.1671 155079 -
obs0.1693 163270 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.29 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15318 0 186 1715 17219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007815883
X-RAY DIFFRACTIONf_angle_d0.898821521
X-RAY DIFFRACTIONf_chiral_restr0.05472467
X-RAY DIFFRACTIONf_plane_restr0.00742756
X-RAY DIFFRACTIONf_dihedral_angle_d13.39596075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.32392690.25115206X-RAY DIFFRACTION99.91
1.97-20.24362830.2275132X-RAY DIFFRACTION99.93
2-2.020.27882880.21865110X-RAY DIFFRACTION99.85
2.02-2.050.25922960.21025099X-RAY DIFFRACTION99.87
2.05-2.070.2312750.20565216X-RAY DIFFRACTION99.96
2.07-2.10.28032680.21125098X-RAY DIFFRACTION100
2.1-2.130.27122530.19545180X-RAY DIFFRACTION99.96
2.13-2.160.26422400.19735204X-RAY DIFFRACTION99.96
2.16-2.20.26382630.19215179X-RAY DIFFRACTION99.98
2.2-2.230.25032750.19185125X-RAY DIFFRACTION99.91
2.23-2.270.26163030.19355170X-RAY DIFFRACTION99.93
2.27-2.310.25422620.18815138X-RAY DIFFRACTION99.87
2.31-2.360.25123110.18545169X-RAY DIFFRACTION99.93
2.36-2.410.24492650.18285107X-RAY DIFFRACTION99.91
2.41-2.460.26372830.1875149X-RAY DIFFRACTION99.76
2.46-2.520.26242470.18865205X-RAY DIFFRACTION99.93
2.52-2.580.24822820.18765140X-RAY DIFFRACTION99.85
2.58-2.650.22952520.18445170X-RAY DIFFRACTION99.87
2.65-2.730.22862540.19295185X-RAY DIFFRACTION99.85
2.73-2.810.27212440.18865211X-RAY DIFFRACTION99.91
2.81-2.910.22542880.17855144X-RAY DIFFRACTION99.87
2.91-3.030.24112690.18135187X-RAY DIFFRACTION99.87
3.03-3.170.23213000.18155137X-RAY DIFFRACTION99.85
3.17-3.340.20922700.17145196X-RAY DIFFRACTION99.89
3.34-3.540.212740.1635123X-RAY DIFFRACTION99.85
3.54-3.820.18432490.14645248X-RAY DIFFRACTION99.93
3.82-4.20.15672820.12785171X-RAY DIFFRACTION99.8
4.2-4.810.14092860.11935175X-RAY DIFFRACTION99.65
4.81-6.060.18772290.14935287X-RAY DIFFRACTION99.89
6.06-42.260.17423310.1565218X-RAY DIFFRACTION99.43
Refinement TLS params.Method: refined / Origin x: -3.86067292567 Å / Origin y: 0.754078944801 Å / Origin z: 23.0618749266 Å
111213212223313233
T0.258914879837 Å20.0176081218118 Å20.00758702862617 Å2-0.208945737884 Å2-0.0129631354871 Å2--0.258857319509 Å2
L0.0279360740815 °20.0734370276599 °20.0927158986614 °2--0.0135784778891 °20.0882795068789 °2--0.382014866712 °2
S0.00341577397748 Å °0.00175517227866 Å °0.0235165393625 Å °-0.0335547505165 Å °-0.0275157547827 Å °-0.0129501912434 Å °0.0258202450875 Å °-0.0535501049882 Å °0.0252134291867 Å °
Refinement TLS groupSelection details: all

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