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- PDB-1mhd: CRYSTAL STRUCTURE OF A SMAD MH1 DOMAIN BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1mhd
TitleCRYSTAL STRUCTURE OF A SMAD MH1 DOMAIN BOUND TO DNA
Components
  • (DNA) x 2
  • SMAD3
KeywordsCOMPLEX (TRANSCRIPTION ACTIVATOR/DNA) / COMPLEX (TRANSCRIPTION ACTIVATOR-DNA) / SMAD3 MH1 / SMAD BINDING ELEMENT / DNA / COMPLEX (TRANSCRIPTION ACTIVATOR-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 / FOXO-mediated transcription of cell cycle genes / DEAD/H-box RNA helicase binding / positive regulation of chondrocyte differentiation / regulation of transforming growth factor beta receptor signaling pathway / 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 / transforming growth factor beta receptor binding / Germ layer formation at gastrulation / primary miRNA processing / Formation of definitive endoderm / SMAD protein signal transduction / 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 / I-SMAD binding / Interleukin-37 signaling / cell-cell junction organization / TGFBR3 expression / nuclear inner membrane / negative regulation of ossification / positive regulation of positive chemotaxis / osteoblast development / NOTCH4 Intracellular Domain Regulates Transcription / RUNX3 regulates CDKN1A transcription / signal transduction involved in regulation of gene expression / ureteric bud development / negative regulation of cardiac muscle hypertrophy in response to stress / adrenal gland development / DNA-binding transcription repressor activity / negative regulation of cytosolic calcium ion concentration / negative regulation of fat cell differentiation / heart looping / R-SMAD binding / TGF-beta receptor signaling activates SMADs / thyroid gland development / mesoderm formation / positive regulation of SMAD protein signal transduction / developmental growth / negative regulation of cell differentiation / anatomical structure morphogenesis / positive regulation of focal adhesion assembly / negative regulation of osteoblast differentiation / regulation of immune response / positive regulation of bone mineralization / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / somitogenesis / phosphatase binding / positive regulation of epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / cis-regulatory region sequence-specific DNA binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / collagen binding / positive regulation of stress fiber assembly / extrinsic apoptotic signaling pathway / JNK cascade / negative regulation of miRNA transcription / transforming growth factor beta receptor signaling pathway / T cell activation / liver development / release of cytochrome c from mitochondria / Downregulation of TGF-beta receptor signaling / ubiquitin binding / positive regulation of interleukin-1 beta production / transcription corepressor binding / nuclear receptor binding / regulation of mitochondrial membrane potential / cellular response to glucose stimulus / apoptotic signaling pathway
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 / MIR / Resolution: 2.8 Å
AuthorsShi, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-beta signaling.
Authors: Shi, Y. / Wang, Y.F. / Jayaraman, L. / Yang, H. / Massague, J. / Pavletich, N.P.
History
DepositionAug 18, 1998Processing site: NDB
Revision 1.0Aug 18, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
C: DNA
D: DNA
A: SMAD3
B: SMAD3


Theoretical massNumber of molelcules
Total (without water)39,3334
Polymers39,3334
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.600, 60.400, 71.600
Angle α, β, γ (deg.)90.00, 102.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA


Mass: 3959.612 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA


Mass: 4294.814 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein SMAD3 / SMAD N-DOMAIN


Mass: 15539.169 Da / Num. of mol.: 2 / Fragment: MH1 DOMAIN, RESIDUES 1 - 144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: SMAD / Plasmid: PGEX / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P84022
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 36 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMcitrate1reservoir
228 %PEG20001reservoir
3100 mMammonium acetate1reservoir
45 mM1reservoirMgCl2
520 mMdithiothreitol1reservoir
61 mMprotein1drop

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 5, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 9228 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rsym value: 0.053 / Net I/σ(I): 33
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 9 / Rsym value: 0.162 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 39338 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 96.5 % / Rmerge(I) obs: 0.162

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→8 Å / Cross valid method: R FACTOR / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.288 402 5 %RANDOM
Rwork0.212 ---
obs0.212 8490 93.6 %-
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 548 0 24 2614
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.734
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.382 39 5 %
Rwork0.34 870 -
obs--81.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.34

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