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- PDB-1u7v: Crystal Structure of the phosphorylated Smad2/Smad4 heterotrimeri... -

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Basic information

Entry
Database: PDB / ID: 1u7v
TitleCrystal Structure of the phosphorylated Smad2/Smad4 heterotrimeric complex
Components
  • Mothers against decapentaplegic homolog 2
  • Mothers against decapentaplegic homolog 4
KeywordsSIGNALING PROTEIN / Smad / TGF-beta / signal transduction / protein complex / phosphorylation
Function / homology
Function and homology information


paraxial mesoderm morphogenesis / : / zygotic specification of dorsal/ventral axis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / activin responsive factor complex / atrioventricular valve formation / nodal signaling pathway / SMAD4 MH2 Domain Mutants in Cancer ...paraxial mesoderm morphogenesis / : / zygotic specification of dorsal/ventral axis / negative regulation of cardiac myofibril assembly / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / activin responsive factor complex / atrioventricular valve formation / nodal signaling pathway / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / epithelial cell migration / SMAD protein complex / neuron fate specification / co-SMAD binding / cardiac muscle hypertrophy in response to stress / 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 / determination of left/right asymmetry in lateral mesoderm / response to transforming growth factor beta / regulation of transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of cell cycle genes / odontoblast differentiation / trophoblast cell migration / secondary palate development / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / left ventricular cardiac muscle tissue morphogenesis / cardiac conduction system development / positive regulation of extracellular matrix assembly / atrioventricular canal development / Transcriptional regulation of pluripotent stem cells / sulfate binding / negative regulation of cardiac muscle hypertrophy / anterior/posterior pattern specification / Germ layer formation at gastrulation / primary miRNA processing / SMAD protein signal transduction / cellular response to BMP stimulus / pulmonary valve morphogenesis / transforming growth factor beta receptor binding / Formation of definitive endoderm / Signaling by BMP / Signaling by Activin / activin receptor signaling pathway / negative regulation of ossification / type I transforming growth factor beta receptor binding / positive regulation of BMP signaling pathway / Formation of axial mesoderm / ureteric bud development / outflow tract septum morphogenesis / Signaling by NODAL / endocardial cushion morphogenesis / mesoderm formation / response to cholesterol / adrenal gland development / I-SMAD binding / embryonic digit morphogenesis / TGFBR3 expression / aortic valve morphogenesis / Cardiogenesis / endothelial cell activation / RUNX3 regulates CDKN1A transcription / ventricular septum morphogenesis / interleukin-6-mediated signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / ovarian follicle development / cell fate commitment / SMAD binding / R-SMAD binding / TGF-beta receptor signaling activates SMADs / negative regulation of cell differentiation / positive regulation of SMAD protein signal transduction / ERK1 and ERK2 cascade / BMP signaling pathway / epithelial to mesenchymal transition / gastrulation / cellular response to transforming growth factor beta stimulus / transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / anatomical structure morphogenesis / positive regulation of cardiac muscle cell apoptotic process / positive regulation of epithelial to mesenchymal transition / extrinsic apoptotic signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / phosphatase binding / cis-regulatory region sequence-specific DNA binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / collagen binding / transcription corepressor binding / Downregulation of TGF-beta receptor signaling / cellular response to glucose stimulus / negative regulation of protein catabolic process / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade
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 4 / SMAD family member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 4, 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 1.4Oct 16, 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 2
C: Mothers against decapentaplegic homolog 2
B: Mothers against decapentaplegic homolog 4


Theoretical massNumber of molelcules
Total (without water)70,7343
Polymers70,7343
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-27 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.240, 59.951, 207.418
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 2 / SMAD 2 / Mothers against DPP homolog 2 / Mad-related protein 2 / hMAD-2 / JV18-1 / hSMAD2


Mass: 22499.336 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: SMAD2, MADH2, MADR2 / Plasmid: pTXB-1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q15796
#2: Protein Mothers against decapentaplegic homolog 4 / SMAD 4 / Mothers against DPP homolog 4 / Deletion target in pancreatic carcinoma 4 / hSMAD4


Mass: 25735.330 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
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.16 %
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

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 10, 2002 / Details: mirrors
RadiationMonochromator: Ni filter/Osmic mirror / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. all: 17632 / Num. obs: 14546 / % possible obs: 82.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.7
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1353 / % possible all: 84.4

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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: 2.7→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
Rfree0.279 1485 -random
Rwork0.243 ---
all-17632 --
obs-14546 82.5 %-
Displacement parametersBiso mean: 67.6 Å2
Refinement stepCycle: LAST / Resolution: 2.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4777 0 0 0 4777
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_bond_d0.011
LS refinement shellResolution: 2.7→2.8 Å
RfactorNum. reflection% reflection
Rfree0.279 --
Rwork0.243 --
obs-1353 85.3 %

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