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- PDB-1ygs: CRYSTAL STRUCTURE OF THE SMAD4 TUMOR SUPPRESSOR C-TERMINAL DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1ygs
TitleCRYSTAL STRUCTURE OF THE SMAD4 TUMOR SUPPRESSOR C-TERMINAL DOMAIN
ComponentsSMAD4
KeywordsTUMOUR SUPPRESSOR / SMAD4 / TUMOR SUPPRESSOR C-TERMINAL DOMAIN / TGF-BETA SIGNAL MEDIATOR / BETA-SANDWICH SCAFFOLD WITH A THREE-HELIX BUNDLE
Function / homology
Function and homology information


positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / activin responsive factor complex / RUNX3 regulates BCL2L11 (BIM) transcription / mesendoderm development ...positive regulation of cell proliferation involved in heart valve morphogenesis / female gonad morphogenesis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / somite rostral/caudal axis specification / atrioventricular valve formation / activin responsive factor complex / RUNX3 regulates BCL2L11 (BIM) transcription / mesendoderm development / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / regulation of hair follicle development / sebaceous gland development / filamin binding / SMAD protein complex / positive regulation of luteinizing hormone secretion / formation of anatomical boundary / RUNX2 regulates bone development / epithelial cell migration / regulation of transforming growth factor beta2 production / heteromeric SMAD protein complex / positive regulation of follicle-stimulating hormone secretion / endocardial cell differentiation / neuron fate specification / epithelial to mesenchymal transition involved in endocardial cushion formation / response to transforming growth factor beta / FOXO-mediated transcription of cell cycle genes / secondary palate development / brainstem development / negative regulation of cardiac muscle hypertrophy / left ventricular cardiac muscle tissue morphogenesis / Transcriptional regulation of pluripotent stem cells / atrioventricular canal development / cardiac conduction system development / outflow tract septum morphogenesis / positive regulation of extracellular matrix assembly / sulfate binding / Germ layer formation at gastrulation / cellular response to BMP stimulus / Signaling by BMP / Formation of definitive endoderm / activin receptor signaling pathway / SMAD protein signal transduction / Signaling by Activin / Signaling by NODAL / cardiac muscle hypertrophy in response to stress / TGFBR3 expression / gastrulation with mouth forming second / I-SMAD binding / endothelial cell activation / neural crest cell differentiation / Cardiogenesis / RUNX3 regulates CDKN1A transcription / adrenal gland development / embryonic digit morphogenesis / branching involved in ureteric bud morphogenesis / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / positive regulation of cardiac muscle cell apoptotic process / seminiferous tubule development / positive regulation of transforming growth factor beta receptor signaling pathway / TGF-beta receptor signaling activates SMADs / uterus development / R-SMAD binding / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / developmental growth / single fertilization / anatomical structure morphogenesis / BMP signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / positive regulation of epithelial to mesenchymal transition / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / ovarian follicle development / cellular response to transforming growth factor beta stimulus / extrinsic apoptotic signaling pathway / collagen binding / ERK1 and ERK2 cascade / transforming growth factor beta receptor signaling pathway / transcription corepressor binding / axon guidance / cellular response to glucose stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / transcription coactivator binding / positive regulation of miRNA transcription / osteoblast differentiation / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / intracellular iron ion homeostasis / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding
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
Mothers against decapentaplegic homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsShi, Y. / Hata, A. / Lo, R.S. / Massague, J. / Pavletich, N.P.
CitationJournal: Nature / Year: 1997
Title: A structural basis for mutational inactivation of the tumour suppressor Smad4.
Authors: Shi, Y. / Hata, A. / Lo, R.S. / Massague, J. / Pavletich, N.P.
History
DepositionOct 3, 1997Processing site: BNL
Revision 1.0Jul 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMAD4


Theoretical massNumber of molelcules
Total (without water)25,5111
Polymers25,5111
Non-polymers00
Water2,486138
1
A: SMAD4

A: SMAD4

A: SMAD4


Theoretical massNumber of molelcules
Total (without water)76,5333
Polymers76,5333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation83_555y,-z+1/2,-x+1/21
crystal symmetry operation32_555-z+1/2,x,-y+1/21
Unit cell
Length a, b, c (Å)197.842, 197.842, 197.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein SMAD4 / DPC4 / HMAD4 / MADR4


Mass: 25511.090 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 319 - 552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 (DE3)
Cellular location: CYTOPLASM (CAN BE TRANSLOCATED INTO NUCLEUS)
Plasmid: BL21 / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13485
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.16 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.5
Details: 100 MM NAMES, PH6.5, 25% PEG MONOMETHYLETHER 5000, 5 MM DTT, 200 MM (NH4)2SO4
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 mg/mlprotein1drop
2100 mMMES1reservoir
325 %mPEG50001reservoir
4200 mMammonium sulfate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorDetector: CCD / Date: Jul 4, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. obs: 18650 / % possible obs: 93.5 % / Observed criterion σ(I): 1.5 / Redundancy: 5.2 % / Rsym value: 0.039 / Net I/σ(I): 32
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 9.9 / Rsym value: 0.162 / % possible all: 93.1
Reflection
*PLUS
Num. measured all: 30691 / Rmerge(I) obs: 0.065

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Processing

Software
NameClassification
DMmodel building
SQUASHphasing
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→6 Å / Cross valid method: R FACTOR / σ(F): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.279 742 5 %RANDOM
Rwork0.219 ---
obs0.219 16157 86.2 %-
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 0 156 1678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.538
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: 2.1→2.19 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.322 90 5 %
Rwork0.316 1677 -
obs--82 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WAT

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