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- PDB-6zvq: Complex between SMAD2 MH2 domain and peptide from Ski corepressor -

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Basic information

Entry
Database: PDB / ID: 6zvq
TitleComplex between SMAD2 MH2 domain and peptide from Ski corepressor
Components
  • Mothers against decapentaplegic homolog 2
  • Ski oncogene
KeywordsTRANSCRIPTION / Phosphoserine / Signal transduction / Transcription modulation
Function / homology
Function and homology information


nose morphogenesis / histone deacetylase inhibitor activity / zygotic specification of dorsal/ventral axis / regulation of binding / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway ...nose morphogenesis / histone deacetylase inhibitor activity / zygotic specification of dorsal/ventral axis / regulation of binding / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / myotube differentiation / endoderm formation / co-SMAD binding / heteromeric SMAD protein complex / determination of left/right asymmetry in lateral mesoderm / odontoblast differentiation / secondary palate development / pericardium development / FOXO-mediated transcription of cell cycle genes / lens morphogenesis in camera-type eye / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / negative regulation of Schwann cell proliferation / Transcriptional regulation of pluripotent stem cells / regulation of transforming growth factor beta receptor signaling pathway / embryonic foregut morphogenesis / primary miRNA processing / transforming growth factor beta receptor binding / Germ layer formation at gastrulation / camera-type eye morphogenesis / olfactory bulb development / pulmonary valve morphogenesis / Signaling by BMP / myelination in peripheral nervous system / type I transforming growth factor beta receptor binding / Formation of definitive endoderm / signal transduction involved in regulation of gene expression / activin receptor signaling pathway / Signaling by Activin / SMAD protein signal transduction / negative regulation of activin receptor signaling pathway / Formation of axial mesoderm / positive regulation of BMP signaling pathway / Signaling by NODAL / response to cholesterol / embryonic cranial skeleton morphogenesis / camera-type eye development / I-SMAD binding / aortic valve morphogenesis / pancreas development / bone morphogenesis / embryonic limb morphogenesis / insulin secretion / face morphogenesis / anterior/posterior axis specification / anterior/posterior pattern specification / cardiac muscle cell proliferation / ureteric bud development / endocardial cushion morphogenesis / organ growth / adrenal gland development / negative regulation of SMAD protein signal transduction / roof of mouth development / SMAD binding / TGF-beta receptor signaling activates SMADs / somatic stem cell population maintenance / R-SMAD binding / mesoderm formation / negative regulation of BMP signaling pathway / positive regulation of Wnt signaling pathway / phosphatase binding / negative regulation of osteoblast differentiation / anatomical structure morphogenesis / cell fate commitment / positive regulation of DNA binding / cis-regulatory region sequence-specific DNA binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / skeletal muscle fiber development / positive regulation of epithelial to mesenchymal transition / negative regulation of fibroblast proliferation / gastrulation / transcription repressor complex / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / post-embryonic development / neural tube closure / cell motility / cellular response to glucose stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of transforming growth factor beta receptor signaling pathway / lung development / tau protein binding / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / disordered domain specific binding / retina development in camera-type eye / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific
Similarity search - Function
: / c-SKI SMAD4-binding domain / Transcription regulator SKI/SnoN / c-SKI Smad4 binding domain / c-SKI Smad4 binding domain / SKI/SNO/DAC domain / Ski-like, DNA-binding domain superfamily / SKI/SNO/DAC family / MAD homology, MH1 / Dwarfin ...: / c-SKI SMAD4-binding domain / Transcription regulator SKI/SnoN / c-SKI Smad4 binding domain / c-SKI Smad4 binding domain / SKI/SNO/DAC domain / Ski-like, DNA-binding domain superfamily / SKI/SNO/DAC family / MAD homology, MH1 / Dwarfin / SMAD MH1 domain superfamily / MAD homology domain 1 (MH1) profile. / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins / SMAD-like domain superfamily / SAND-like domain superfamily / Putative DNA-binding domain superfamily / SMAD/FHA domain superfamily
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Ski oncogene / Mothers against decapentaplegic homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsPurkiss, A.G. / Kjaer, S. / George, R. / Hill, C.S.
CitationJournal: Elife / Year: 2021
Title: Mutations in SKI in Shprintzen-Goldberg syndrome lead to attenuated TGF-beta responses through SKI stabilization.
Authors: Gori, I. / George, R. / Purkiss, A.G. / Strohbuecker, S. / Randall, R.A. / Ogrodowicz, R. / Carmignac, V. / Faivre, L. / Joshi, D. / Kjaer, S. / Hill, C.S.
History
DepositionJul 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 2
B: Ski oncogene
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,76615
Polymers29,3872
Non-polymers1,37913
Water1,36976
1
A: Mothers against decapentaplegic homolog 2
B: Ski oncogene
hetero molecules

A: Mothers against decapentaplegic homolog 2
B: Ski oncogene
hetero molecules

A: Mothers against decapentaplegic homolog 2
B: Ski oncogene
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,29845
Polymers88,1616
Non-polymers4,13739
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Buried area23060 Å2
ΔGint-176 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.820, 113.820, 113.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11A-664-

HOH

21A-672-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Mothers against decapentaplegic homolog 2 / Mothers against DPP homolog 2 / JV18-1 / Mad-related protein 2 / hMAD-2 / SMAD family member 2 / hSMAD2


Mass: 25540.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD2, MADH2, MADR2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15796
#2: Protein/peptide Ski oncogene / Proto-oncogene c-Ski


Mass: 3846.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P12755

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Non-polymers , 4 types, 89 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.449 Å3/Da / Density % sol: 49.809 % / Description: Cubic crystals in phase separation droplets
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.5M Ammonium Sulphate, 0.15M Sodium Potassium Tartrate, 0.08M Tri-Sodium Citrate pH 5.6, 25% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2017 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.03→56.91 Å / Num. obs: 15983 / % possible obs: 99.95 % / Redundancy: 10 % / Biso Wilson estimate: 37.09 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.04167 / Rrim(I) all: 0.1319 / Net I/σ(I): 12.24
Reflection shellResolution: 2.031→2.104 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.469 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 1565 / CC1/2: 0.635 / CC star: 0.881 / Rpim(I) all: 0.4846 / Rrim(I) all: 1.547 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.18.2_3874refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1khx

1khx


Resolution: 2.03→56.91 Å / SU ML: 0.1886 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7317
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2101 1440 4.69 %
Rwork0.1641 29283 -
obs0.1665 15983 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.13 Å2
Refinement stepCycle: LAST / Resolution: 2.03→56.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 88 76 1927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731902
X-RAY DIFFRACTIONf_angle_d0.91822582
X-RAY DIFFRACTIONf_chiral_restr0.0545280
X-RAY DIFFRACTIONf_plane_restr0.0065327
X-RAY DIFFRACTIONf_dihedral_angle_d13.9009284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.10.28171220.26982938X-RAY DIFFRACTION100
2.1-2.190.3261980.25233008X-RAY DIFFRACTION99.97
2.19-2.290.27351820.20582838X-RAY DIFFRACTION99.9
2.29-2.410.23541620.18632941X-RAY DIFFRACTION100
2.41-2.560.26121020.16362934X-RAY DIFFRACTION99.97
2.56-2.760.24341420.22642956X-RAY DIFFRACTION100
2.76-3.030.24611830.18552886X-RAY DIFFRACTION100
3.04-3.470.2081430.15552948X-RAY DIFFRACTION99.94
3.48-4.370.1881460.11492916X-RAY DIFFRACTION100
4.38-56.910.16871600.14922918X-RAY DIFFRACTION99.81

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