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- PDB-1ozj: Crystal structure of Smad3-MH1 bound to DNA at 2.4 A resolution -

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Basic information

Entry
Database: PDB / ID: 1ozj
TitleCrystal structure of Smad3-MH1 bound to DNA at 2.4 A resolution
Components
  • (Smad binding element) x 2
  • SMAD 3
KeywordsTRANSCRIPTION/DNA / Smad / Mad homology domain 1 / DNA recognition / TGF-beta signaling / zinc-binding module / TRANSCRIPTION-DNA COMPLEX
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 / transdifferentiation / paraxial mesoderm morphogenesis / 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 / transdifferentiation / paraxial mesoderm morphogenesis / 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 / heteromeric SMAD protein complex / pericardium development / co-SMAD binding / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / bHLH transcription factor binding / DEAD/H-box RNA helicase binding / FOXO-mediated transcription of cell cycle genes / regulation of transforming growth factor beta receptor signaling pathway / positive regulation of chondrocyte differentiation / negative regulation of osteoblast proliferation / trophoblast cell migration / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of extracellular matrix assembly / negative regulation of wound healing / embryonic foregut morphogenesis / nuclear glucocorticoid receptor binding / lens fiber cell differentiation / Germ layer formation at gastrulation / primary miRNA processing / transforming growth factor beta receptor binding / SMAD protein signal transduction / Formation of definitive endoderm / embryonic pattern specification / endoderm development / Signaling by Activin / embryonic cranial skeleton morphogenesis / activin receptor signaling pathway / Formation of axial mesoderm / response to angiotensin / Signaling by NODAL / regulation of epithelial cell proliferation / Interleukin-37 signaling / cell-cell junction organization / I-SMAD binding / TGFBR3 expression / nuclear inner membrane / negative regulation of ossification / positive regulation of positive chemotaxis / NOTCH4 Intracellular Domain Regulates Transcription / RUNX3 regulates CDKN1A transcription / osteoblast development / signal transduction involved in regulation of gene expression / ureteric bud development / DNA-binding transcription repressor activity / adrenal gland development / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cytosolic calcium ion concentration / negative regulation of fat cell differentiation / heart looping / TGF-beta receptor signaling activates SMADs / thyroid gland development / R-SMAD binding / mesoderm formation / positive regulation of SMAD protein signal transduction / anatomical structure morphogenesis / negative regulation of cell differentiation / developmental growth / positive regulation of focal adhesion assembly / regulation of immune response / negative regulation of osteoblast differentiation / positive regulation of bone mineralization / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / somitogenesis / phosphatase binding / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / cis-regulatory region sequence-specific DNA binding / collagen binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of stress fiber assembly / JNK cascade / extrinsic apoptotic signaling pathway / transforming growth factor beta receptor signaling pathway / negative regulation of miRNA transcription / T cell activation / release of cytochrome c from mitochondria / Downregulation of TGF-beta receptor signaling / positive regulation of interleukin-1 beta production / ubiquitin binding / nuclear receptor binding / transcription corepressor binding / regulation of mitochondrial membrane potential / cellular response to glucose stimulus / apoptotic signaling pathway / promoter-specific chromatin binding
Similarity search - Function
Smad3; Chain A / SMAD MH1 domain / 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 ...Smad3; Chain A / SMAD MH1 domain / 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 / SMAD/FHA domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Mothers against decapentaplegic homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChai, J. / Wu, J.-W. / Yan, N. / Massague, J. / Pavletich, N.P. / Shi, Y.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Features of a Smad3 MH1-DNA complex. Roles of water and zinc in DNA binding.
Authors: Chai, J. / Wu, J.-W. / Yan, N. / Massague, J. / Pavletich, N.P. / Shi, Y.
History
DepositionApr 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Smad binding element
D: Smad binding element
A: SMAD 3
B: SMAD 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0036
Polymers42,8734
Non-polymers1312
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.6, 60.4, 71.6
Angle α, β, γ (deg.)90, 102, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain Smad binding element


Mass: 4552.986 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain Smad binding element


Mass: 4624.021 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein SMAD 3 / Mothers against DPP homolog 3 / Mad3 / hMAD-3 / mMad3 / JV15-2 / hSMAD3


Mass: 16847.787 Da / Num. of mol.: 2 / Fragment: DWA DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MADH3 OR SMAD3 OR MAD3 / Production host: Escherichia coli (E. coli) / References: UniProt: P84022
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: citrate, PEG2000, ammonium acetate, spermine, magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1citrate11
2PEG20011
3ammonium acetate11
4spermine11
5magnesium chloride11
6ammonium acetate12
7magnesium chloride12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Shi, Y., (1998) Cell, 94, 585.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM1reservoir
228 %PEG20001reservoir
3100 mM1reservoir
45 mM1reservoirMgCl2
520 mMdithiothreitol1reservoir
61 mMprotein1drop
71

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 2002
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→99 Å / Num. all: 14974 / Num. obs: 14360 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.4→2.5 Å / % possible all: 82.5
Reflection
*PLUS
Lowest resolution: 99 Å / Redundancy: 4.8 % / Num. measured all: 68907 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 82.5 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 5.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→15 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.27 675 random
Rwork0.21 --
all0.22 14891 -
obs-13219 -
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 609 2 47 2730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_bond_d0.005
Refinement
*PLUS
Rfactor Rfree: 0.27 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.265

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