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- PDB-1u7f: Crystal Structure of the phosphorylated Smad3/Smad4 heterotrimeri... -

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Basic information

Entry
Database: PDB / ID: 1u7f
TitleCrystal Structure of the phosphorylated Smad3/Smad4 heterotrimeric complex
Components
  • Mothers against decapentaplegic homolog 3
  • Mothers against decapentaplegic homolog 4
KeywordsSIGNALING PROTEIN / Smad / TGF-beta / signal transduction / protein complex / phosphorylation
Function / homology
Function and homology information


nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / : / negative regulation of cardiac myofibril assembly / positive regulation of transforming growth factor beta3 production / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / sterol response element binding / activin responsive factor complex ...nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / : / negative regulation of cardiac myofibril assembly / positive regulation of transforming growth factor beta3 production / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / sterol response element binding / activin responsive factor complex / atrioventricular valve formation / transdifferentiation / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / epithelial cell migration / SMAD protein complex / negative regulation of osteoblast proliferation / neuron fate specification / co-SMAD binding / heteromeric SMAD protein complex / RUNX2 regulates bone development / filamin binding / regulation of transforming growth factor beta2 production / RUNX3 regulates BCL2L11 (BIM) transcription / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / response to transforming growth factor beta / DEAD/H-box RNA helicase binding / FOXO-mediated transcription of cell cycle genes / bHLH transcription factor binding / trophoblast cell migration / negative regulation of transforming growth factor beta production / secondary palate development / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / left ventricular cardiac muscle tissue morphogenesis / positive regulation of chondrocyte differentiation / cardiac conduction system development / positive regulation of extracellular matrix assembly / negative regulation of wound healing / atrioventricular canal development / Transcriptional regulation of pluripotent stem cells / sulfate binding / negative regulation of cardiac muscle hypertrophy / nuclear glucocorticoid receptor binding / cardiac muscle hypertrophy in response to stress / Germ layer formation at gastrulation / SMAD protein signal transduction / primary miRNA processing / cellular response to BMP stimulus / negative regulation of lipopolysaccharide-mediated signaling pathway / cell-cell junction organization / transforming growth factor beta receptor binding / Signaling by BMP / Formation of definitive endoderm / signal transduction involved in regulation of gene expression / response to angiotensin / Signaling by Activin / negative regulation of ossification / activin receptor signaling pathway / Formation of axial mesoderm / regulation of dendritic spine morphogenesis / outflow tract septum morphogenesis / ureteric bud development / Signaling by NODAL / Interleukin-37 signaling / I-SMAD binding / adrenal gland development / response to alcohol / TGFBR3 expression / embryonic digit morphogenesis / positive regulation of positive chemotaxis / NOTCH4 Intracellular Domain Regulates Transcription / Cardiogenesis / endothelial cell activation / RUNX3 regulates CDKN1A transcription / nuclear inner membrane / negative regulation of fat cell differentiation / DNA-binding transcription repressor activity / ventricular septum morphogenesis / negative regulation of cardiac muscle hypertrophy in response to stress / interleukin-6-mediated signaling pathway / positive regulation of bone mineralization / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of cytosolic calcium ion concentration / R-SMAD binding / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / BMP signaling pathway / positive regulation of focal adhesion assembly / cellular response to transforming growth factor beta stimulus / ovarian follicle development / JNK cascade / regulation of immune response / negative regulation of cell differentiation / ERK1 and ERK2 cascade / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / anatomical structure morphogenesis
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 / SMAD family member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChacko, B.M. / Qin, B.Y. / Tiwari, A. / Shi, G. / Lam, S. / Hayward, L.J. / de Caestecker, M. / Lin, K.
CitationJournal: Mol.Cell / Year: 2004
Title: Structural basis of heteromeric smad protein assembly in tgf-Beta signaling
Authors: Chacko, B.M. / Qin, B.Y. / Tiwari, A. / Shi, G. / Lam, S. / Hayward, L.J. / De Caestecker, M. / Lin, K.
History
DepositionAug 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mothers against decapentaplegic homolog 3
B: Mothers against decapentaplegic homolog 4
C: Mothers against decapentaplegic homolog 3


Theoretical massNumber of molelcules
Total (without water)70,9953
Polymers70,9953
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-26 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.471, 60.545, 205.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mothers against decapentaplegic homolog 3 / SMAD 3 / Mothers against DPP homolog 3 / Mad3 / hMAD-3 / JV15-2 / hSMAD3


Mass: 22467.271 Da / Num. of mol.: 2 / Fragment: MH2 and Linker domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD3, MADH3 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P84022
#2: Protein Mothers against decapentaplegic homolog 4 / SMAD 4 / Mothers against DPP homolog 4 / Deletion target in pancreatic carcinoma 4 / hSMAD4


Mass: 26060.693 Da / Num. of mol.: 1 / Fragment: MH2 and Linker domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD4, MADH4, DPC4 / Plasmid: pGEX-4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q13485
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Tris-HCl, 0-15 mM magnesium chloride, 5-15% ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C11
ROTATING ANODERIGAKU RU30021.5418
Detector
TypeIDDetectorDateDetails (eV)
ADSC QUANTUM 41CCDMar 8, 2003mirrors
RIGAKU RAXIS IV2IMAGE PLATEAug 7, 2002mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Ni filter/Osmic mirrorMADMx-ray1
2Ni filter/Osmic mirrorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.54181
ReflectionResolution: 2.5→100 Å / Num. all: 21793 / Num. obs: 20128 / % possible obs: 92.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 27.5
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 3 / Num. unique all: 1110 / % possible all: 87.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KHX

1khx


Resolution: 2.6→100 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 967 -random
Rwork0.232 ---
all-20128 --
obs-19161 92.4 %-
Displacement parametersBiso mean: 64 Å2
Refinement stepCycle: LAST / Resolution: 2.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4728 0 0 255 4983
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_bond_d0.008
LS refinement shellResolution: 2.6→2.69 Å
RfactorNum. reflection% reflection
Rfree0.246 181 -
Rwork0.232 --
obs-1110 96.5 %

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