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- PDB-7tyg: Structure of the human leucine rich repeat protein SHOC2, residue... -

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Basic information

Entry
Database: PDB / ID: 7tyg
TitleStructure of the human leucine rich repeat protein SHOC2, residues 80-582
ComponentsLeucine-rich repeat protein SHOC-2
KeywordsHYDROLASE / RAS / PP1 / SHOC2 / LRR
Function / homology
Function and homology information


cellular response to growth hormone stimulus / protein phosphatase type 1 complex / negative regulation of neural precursor cell proliferation / nerve growth factor signaling pathway / 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 / negative regulation of neuron differentiation ...cellular response to growth hormone stimulus / protein phosphatase type 1 complex / negative regulation of neural precursor cell proliferation / nerve growth factor signaling pathway / 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 / negative regulation of neuron differentiation / fibroblast growth factor receptor signaling pathway / positive regulation of neuron differentiation / RAF activation / positive regulation of neuron projection development / protein phosphatase binding / Ras protein signal transduction / signal transduction / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Leucine-rich repeat protein SHOC-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDhembi, A. / Clark, K. / King, D.A.
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 13, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,4993
Polymers113,4752
Non-polymers241
Water11,259625
1
A: Leucine-rich repeat protein SHOC-2


Theoretical massNumber of molelcules
Total (without water)56,7381
Polymers56,7381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leucine-rich repeat protein SHOC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7622
Polymers56,7381
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.350, 102.880, 120.830
Angle α, β, γ (deg.)90.000, 101.738, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 56737.582 Da / Num. of mol.: 2 / Fragment: residues 80-582
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris-Cl(8.0), 0.2 M MgCl2, 11% PEG4K, 2.5% 1,5-diaminopentane

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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 EIGER X 9M / Detector: PIXEL / Date: Dec 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.895→118.303 Å / Num. obs: 82107 / % possible obs: 94.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.29 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.061 / Net I/σ(I): 13
Reflection shellResolution: 1.895→1.902 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2 / Num. unique obs: 869 / CC1/2: 0.748 / Rrim(I) all: 0.644 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHASER1.18.2_3874+SVNphasing
Coot0.96 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZH

4tzh


Resolution: 1.9→41.44 Å / SU ML: 0.2322 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.4087
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2258 4119 5.02 %
Rwork0.1879 77966 -
obs0.1898 82085 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7788 0 1 625 8414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00667902
X-RAY DIFFRACTIONf_angle_d0.858310709
X-RAY DIFFRACTIONf_chiral_restr0.05421303
X-RAY DIFFRACTIONf_plane_restr0.00691366
X-RAY DIFFRACTIONf_dihedral_angle_d13.69863067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.910.285970.24662086X-RAY DIFFRACTION94.3
1.92-1.940.26531190.24151934X-RAY DIFFRACTION97.67
1.94-1.970.3069600.23041276X-RAY DIFFRACTION44.7
1.97-1.990.28531440.22652796X-RAY DIFFRACTION99.93
1.99-2.020.29341510.22742853X-RAY DIFFRACTION99.9
2.02-2.050.28561710.23152779X-RAY DIFFRACTION99.93
2.05-2.080.27231700.21872833X-RAY DIFFRACTION99.8
2.08-2.110.26891180.21022820X-RAY DIFFRACTION99.93
2.11-2.150.25151580.2042869X-RAY DIFFRACTION99.9
2.15-2.180.25891530.20192799X-RAY DIFFRACTION99.97
2.18-2.220.23561480.20472868X-RAY DIFFRACTION99.93
2.22-2.260.27411460.20282761X-RAY DIFFRACTION99.62
2.26-2.310.25431600.2032807X-RAY DIFFRACTION99.73
2.31-2.360.27591380.20522862X-RAY DIFFRACTION99.83
2.36-2.420.26031460.20962822X-RAY DIFFRACTION99.83
2.42-2.480.24441520.20762850X-RAY DIFFRACTION99.8
2.48-2.540.27321390.21282821X-RAY DIFFRACTION99.8
2.54-2.620.27861500.21512841X-RAY DIFFRACTION99.63
2.62-2.70.25961540.21912795X-RAY DIFFRACTION99.53
2.7-2.80.28661360.21062828X-RAY DIFFRACTION99.63
2.8-2.910.24591550.2092842X-RAY DIFFRACTION99.63
2.91-3.040.23131500.21322861X-RAY DIFFRACTION99.7
3.04-3.20.24851260.21272807X-RAY DIFFRACTION99.22
3.2-3.40.26731710.2072820X-RAY DIFFRACTION99.14
3.4-3.670.2271190.18762336X-RAY DIFFRACTION81.62
3.67-4.040.18751180.15882428X-RAY DIFFRACTION84.75
4.04-4.620.1621690.14092816X-RAY DIFFRACTION99.53
4.62-5.820.18451520.15552852X-RAY DIFFRACTION99.54
5.82-41.440.16951490.16092904X-RAY DIFFRACTION99.09
Refinement TLS params.Method: refined / Origin x: -31.3239005291 Å / Origin y: 1.33645829092 Å / Origin z: 28.8237093738 Å
111213212223313233
T0.282771955521 Å20.0110113465734 Å20.014348297155 Å2-0.215797815832 Å2-0.00636757334091 Å2--0.259344433433 Å2
L0.557374380476 °20.088461222098 °20.179752343387 °2-0.185393134206 °20.0564936458084 °2--0.878043077076 °2
S-0.0023078341581 Å °0.155438294435 Å °-0.000512760806388 Å °-0.0146299860773 Å °0.0108528168989 Å °-0.0177329230411 Å °0.0251077541054 Å °0.0310006133066 Å °-0.00911840493193 Å °
Refinement TLS groupSelection details: all

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