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- PDB-1mjs: MH2 domain of transcriptional factor SMAD3 -

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Basic information

Entry
Database: PDB / ID: 1mjs
TitleMH2 domain of transcriptional factor SMAD3
ComponentsSMAD 3
KeywordsTRANSCRIPTION / beta sandwich
Function / homology
Function and homology information


nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / sterol response element binding / paraxial mesoderm morphogenesis / transdifferentiation / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / sterol response element binding / paraxial mesoderm morphogenesis / transdifferentiation / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / immune system development / regulation of striated muscle tissue development / pericardium development / co-SMAD binding / heteromeric SMAD protein complex / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / DEAD/H-box RNA helicase binding / FOXO-mediated transcription of cell cycle genes / bHLH transcription factor binding / regulation of transforming growth factor beta receptor signaling pathway / trophoblast cell migration / negative regulation of osteoblast proliferation / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of chondrocyte differentiation / embryonic foregut morphogenesis / lens fiber cell differentiation / positive regulation of extracellular matrix assembly / negative regulation of wound healing / endoderm development / nuclear glucocorticoid receptor binding / SMAD protein signal transduction / Germ layer formation at gastrulation / primary miRNA processing / transforming growth factor beta receptor binding / cell-cell junction organization / Formation of definitive endoderm / embryonic cranial skeleton morphogenesis / regulation of epithelial cell proliferation / Signaling by Activin / embryonic pattern specification / activin receptor signaling pathway / response to angiotensin / Formation of axial mesoderm / regulation of dendritic spine morphogenesis / signal transduction involved in regulation of gene expression / Signaling by NODAL / Interleukin-37 signaling / ureteric bud development / I-SMAD binding / osteoblast development / TGFBR3 expression / negative regulation of ossification / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of positive chemotaxis / RUNX3 regulates CDKN1A transcription / nuclear inner membrane / response to alcohol / adrenal gland development / DNA-binding transcription repressor activity / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of fat cell differentiation / heart looping / thyroid gland development / negative regulation of cytosolic calcium ion concentration / ciliary transition zone / mesoderm formation / R-SMAD binding / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / positive regulation of focal adhesion assembly / developmental growth / negative regulation of cell differentiation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / anatomical structure morphogenesis / regulation of immune response / positive regulation of bone mineralization / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / somitogenesis / negative regulation of osteoblast differentiation / phosphatase binding / extrinsic apoptotic signaling pathway / cis-regulatory region sequence-specific DNA binding / cellular response to platelet-derived growth factor stimulus / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / JNK cascade / collagen binding / positive regulation of stress fiber assembly / transforming growth factor beta receptor signaling pathway / release of cytochrome c from mitochondria / negative regulation of miRNA transcription / nuclear receptor binding / liver development / transcription corepressor binding / regulation of mitochondrial membrane potential / positive regulation of interleukin-1 beta production / response to gamma radiation
Similarity search - Function
Tumour Suppressor Smad4 - #10 / 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 ...Tumour Suppressor Smad4 - #10 / 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 / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
SMAD family member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsQin, B.Y. / Lam, S.S. / Correia, J.J. / Lin, K.
CitationJournal: Genes Dev. / Year: 2002
Title: Smad3 allostery links TGF-beta receptor kinase activation to transcriptional control
Authors: Qin, B.Y. / Lam, S.S. / Correia, J.J. / Lin, K.
History
DepositionAug 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SMAD 3


Theoretical massNumber of molelcules
Total (without water)22,1781
Polymers22,1781
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.325, 54.325, 59.428
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein SMAD 3 / Mad3 / hMAD-3 / mMad3 / JV15-2 / hSMAD3


Mass: 22178.201 Da / Num. of mol.: 1 / Fragment: MH2 domain, residues 229-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD3 / Production host: Escherichia coli (E. coli) / References: UniProt: P84022
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)Chemical formula
1700 mMammonium dihydrogen phosphate1reservoir
220 %ethylene glycol1reservoirpH4.8
320 mMTris1droppH7.4
410 mM1dropNaCl
50.1 mMEDTA1drop
61 mMdithiothreitol1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→25.12 Å / Num. obs: 14765 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.34 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.2
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.53 / Num. unique all: 1203 / % possible all: 0.78
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 14785 / Num. measured all: 64905
Reflection shell
*PLUS
% possible obs: 77.7 % / Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SMAD4 active fragment

Resolution: 1.91→25.12 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.199 500 4.1 %RANDOM
Rwork0.196 ---
obs-14494 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 83.8708 Å2 / ksol: 0.404108 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å21.45 Å20 Å2
2--0.76 Å20 Å2
3----1.53 Å2
Refine analyzeLuzzati coordinate error free: 0.24 Å / Luzzati sigma a free: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.91→25.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 0 195 1593
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.682
X-RAY DIFFRACTIONc_scbond_it2.52
X-RAY DIFFRACTIONc_scangle_it3.942.5
LS refinement shellResolution: 1.91→2.02 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 76 3.9 %
Rwork0.247 1852 -
obs--73.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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